{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2025-12-14T01:33:56.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2025-12-14T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":47513,"title":"DNA Sequence Assembly","description":null,"description_html":"\u003cdiv style = \"text-align: start; line-height: 20.44px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: none solid rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 258px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 406.5px 129px; transform-origin: 406.5px 129px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eDNA fragments are made by DNA sequencer.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eTo find full sequence, we need to concatenate each other using common sequence information.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eSo, when Input sequences are\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(1) ATCGATCGAAGTCATCG\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eGGAAA\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(3)\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e GGAAA\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eGATCGATTACTT\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eCCGAAA\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(2)\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e CCGAAA\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eACCTAAGGGTTCTCAATGAC .\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eOutput sequence is \u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e'ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC' .\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function y = your_fcn_name(x)\r\n y = x;\r\nend","test_suite":"%%\r\nx = {'ATCGATCGAAGTCATCGGGAAA'\r\n 'CCGAAAACCTAAGGGTTCTCAATGAC'\r\n 'GGAAAGATCGATTACTTCCGAAA'};\r\ny_correct ='ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC';\r\nassert(isequal(your_fcn_name(x),y_correct))\r\n\r\n\r\n%%\r\nx = {'GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT'\r\n'GGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC'\r\n'AGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG'\r\n'CATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC'\r\n'ATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC'\r\n'CGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC'\r\n'CGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG'\r\n'GTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG'};\r\ny_correct='GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG';\r\nassert(isequal(your_fcn_name(x),y_correct))\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":71768,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2020-11-15T12:55:39.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2020-11-15T12:40:44.000Z","updated_at":"2025-10-02T20:02:57.000Z","published_at":"2020-11-15T12:40:44.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA fragments are made by DNA sequencer.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eTo find full sequence, we need to concatenate each other using common sequence information.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSo, when Input sequences are\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e(1) ATCGATCGAAGTCATCG\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eGGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(3)\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e GGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eGATCGATTACTT\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eCCGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(2)\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e CCGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eACCTAAGGGTTCTCAATGAC .\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eOutput sequence is \u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e'ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC' .\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":939,"title":"DNA Pattern Match: Performance Metric - Speed","description":"The Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\r\n\r\nAt \u003chttp://imacst.com/issues/volume-3issue-1/ IMACST\u003e the paper \u003chttp://imacst.com/web_documents/1202002.pdf An Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\r\n\r\nMatlab can achieve matching a six pattern set of L=6 in \u003c15 msec (i5/16GB). This is merely a 99.8% time reduction.\r\n\r\n\r\n*Challenge Description:*\r\nDNA is made of letters ACGT, \u003chttp://en.wikipedia.org/wiki/DNA wiki DNA\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\r\n\r\n*Input:* [DNA, DNA_ID, Patterns]\r\n\r\n* DNA is a 1.8M long uint8 row vector of values 0 thru 3.\r\n* DNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\r\n* Patterns is an Nx6 uint8 array where each row corresponds to a search pattern.\r\n\r\n*Output:* Locations\r\n\r\nLocations of all start indices that match any of the patterns\r\n\r\n*Scoring:* Average Time (msec) for a block of L=6 patterns\r\n\r\nExample:\r\n\r\n* DNA= [0 1 2 3 3 2 1 0 1 2 3 3]\r\n* Pattern = [2 3 3 2 1 0]\r\n* Locations = [3]\r\n\r\n*Hints:*\r\n\r\n* Vectorization (Base 4 to Base 10 of 6 character words)\r\n* Bitshift/Reshape to create all words\r\n* Logical Indexing\r\n \r\n\r\nComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza","description_html":"\u003cp\u003eThe Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\u003c/p\u003e\u003cp\u003eAt \u003ca href=\"http://imacst.com/issues/volume-3issue-1/\"\u003eIMACST\u003c/a\u003e the paper \u003ca href=\"http://imacst.com/web_documents/1202002.pdf\"\u003eAn Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003c/a\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\u003c/p\u003e\u003cp\u003eMatlab can achieve matching a six pattern set of L=6 in \u0026lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.\u003c/p\u003e\u003cp\u003e\u003cb\u003eChallenge Description:\u003c/b\u003e\r\nDNA is made of letters ACGT, \u003ca href=\"http://en.wikipedia.org/wiki/DNA\"\u003ewiki DNA\u003c/a\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e [DNA, DNA_ID, Patterns]\u003c/p\u003e\u003cul\u003e\u003cli\u003eDNA is a 1.8M long uint8 row vector of values 0 thru 3.\u003c/li\u003e\u003cli\u003eDNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\u003c/li\u003e\u003cli\u003ePatterns is an Nx6 uint8 array where each row corresponds to a search pattern.\u003c/li\u003e\u003c/ul\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Locations\u003c/p\u003e\u003cp\u003eLocations of all start indices that match any of the patterns\u003c/p\u003e\u003cp\u003e\u003cb\u003eScoring:\u003c/b\u003e Average Time (msec) for a block of L=6 patterns\u003c/p\u003e\u003cp\u003eExample:\u003c/p\u003e\u003cul\u003e\u003cli\u003eDNA= [0 1 2 3 3 2 1 0 1 2 3 3]\u003c/li\u003e\u003cli\u003ePattern = [2 3 3 2 1 0]\u003c/li\u003e\u003cli\u003eLocations = [3]\u003c/li\u003e\u003c/ul\u003e\u003cp\u003e\u003cb\u003eHints:\u003c/b\u003e\u003c/p\u003e\u003cul\u003e\u003cli\u003eVectorization (Base 4 to Base 10 of 6 character words)\u003c/li\u003e\u003cli\u003eBitshift/Reshape to create all words\u003c/li\u003e\u003cli\u003eLogical Indexing\u003c/li\u003e\u003c/ul\u003e\u003cp\u003eComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza\u003c/p\u003e","function_template":"function Locations = find_DNA(DNA, DNA_ID, Patterns)\r\n persistent DNA_ID_loaded % add other DNA created variables\r\n Locations=[];\r\n if isempty(DNA_ID_loaded) || DNA_ID~=DNA_ID_loaded\r\n % Perform initialization actions on DNA vector - optional\r\n DNA_ID_loaded=DNA_ID;\r\n \r\n end % DNA_ID Processing\r\n\r\n\r\n\r\n \r\nend\r\n\r\n\r\n\r\n\r\n","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\n% Functionality Section\r\nPass=1;\r\nw=6;\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=1;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nif isempty(Locations),Pass=0;end\r\nif max(size(Locations))\u003c1024,Pass=0;end\r\nfor i=1:size(Locations,1)\r\n Pass=Pass \u0026\u0026 ismember(DNA(Locations(i,end):Locations(i,end)+w-1),Patterns,'rows');\r\n end\r\n\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,24,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:12,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=2;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nif isempty(Locations),Pass=0;end\r\nif max(size(Locations))\u003c1024,Pass=0;end\r\nfor i=1:size(Locations,1)\r\n Pass=Pass \u0026\u0026 ismember(DNA(Locations(i,end):Locations(i,end)+w-1),Patterns,'rows');\r\n end\r\n\r\n\r\nassert(isequal(Pass,1))\r\n%%\r\n% Timing Section\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=1;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt1=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 1 Time = %i msec\\n',floor(dt1))\r\n\r\n\r\nPatterns=randi(4,24,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:12,:); % Take first 12 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt2=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 2 Time = %i msec\\n',floor(dt2))\r\n\r\n\r\n% New DNA Set\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=2;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt3=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 3 Time = %i msec\\n',floor(dt3))\r\n\r\n\r\nfeval(@assignin,'caller','score',min(400,floor(double(dt1+dt2+dt3)/30)));\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":9,"test_suite_updated_at":"2012-09-10T03:41:37.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-09-10T00:09:00.000Z","updated_at":"2025-11-21T09:02:33.000Z","published_at":"2012-09-10T03:40:23.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAt\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://imacst.com/issues/volume-3issue-1/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eIMACST\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e the paper\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://imacst.com/web_documents/1202002.pdf\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAn Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eMatlab can achieve matching a six pattern set of L=6 in \u0026lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eChallenge Description:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e DNA is made of letters ACGT,\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/DNA\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ewiki DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [DNA, DNA_ID, Patterns]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is a 1.8M long uint8 row vector of values 0 thru 3.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003ePatterns is an Nx6 uint8 array where each row corresponds to a search pattern.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Locations\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLocations of all start indices that match any of the patterns\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScoring:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Average Time (msec) for a block of L=6 patterns\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA= [0 1 2 3 3 2 1 0 1 2 3 3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003ePattern = [2 3 3 2 1 0]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLocations = [3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eHints:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eVectorization (Base 4 to Base 10 of 6 character words)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eBitshift/Reshape to create all words\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLogical Indexing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches. \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n ACGTCGGCCATGGACATTACG\r\n ACGTCGGCCAsssssssssss\r\n sssssGGCCATGGACATssss\r\n ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":47658,"title":"Calculate the similarity between DNA sequences ","description":null,"description_html":"\u003cdiv style = \"text-align: start; line-height: 20.44px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: none solid rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 453px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 226.5px; transform-origin: 407px 226.5px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 168px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 84px; text-align: left; transform-origin: 384px 84px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eA DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular'' chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eRapid DNA sequencing machinary produces short strands of DNA, and these can be arbitrarily orientated - i.e the DNA strand is 'read' from left to right, or right to left (depends on which side is 'grabbed' when reading starts) , and it comes from either the forward or the reverse complement strand that had been uncoiled to facilitate sequencing.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eHere we are interested in computing the similarity between two strand sequences (called 'reads').\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWe define the similarity in\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eterms of the length of the longest common subsequence LCS, and lengths of the two sequences, LS1 and LS2 respectively.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eSimSeq(S1,S2) = 2*LCS / (LS1+LS2)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWhen S1 = S2 the similarity score is 1.0\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(also when S1 is equal to S2 reverse complement)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWhen the sequences are dissimilar the similarity score approaches zero, as well as when one of the sequences is much longer than the other (alternative definitions that correct for length diffrence are possible, but are of no concern here.)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eNote that the longest common subsequence LCS can be found in the forward or in the reverse complement direction.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eFor instance, LCS('TACCTGAGA','GACCTGAGC') is equal to 7 since the common substring is 'ACCTGAG' in S1, which matches the reverse complement\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e'ACCTGAG' in S2.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function y = SimSeq(s1,s2)\r\n y=0;\r\nend","test_suite":"s1='TACCTGAGAAGG';\r\ns2='TACCTGAGAAGG';\r\ny_correct = 24/24; % LCS is 'TACCTGAGAAGG' \r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='TACCTGAGAAGG';\r\ns2='CCTTCTCAGGTA';\r\ny_correct = 24/24; % LCS is 'TACCTGAGAAGG' in reverse complement\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='TACCTGAGAAGG';\r\ns2='CCCGACCTGAGCACAC';\r\ny_correct = 14/28; % LCS is 'ACCTGAG' \r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='CCTTCTCAGGTA';\r\ns2='CCCGACCTTAGCACAC'; % LCS is 'CCTT' in forward direction or 'AGGT' in reverse complement\r\ny_correct = 8/28;\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='CCTTAAGGTGTA';\r\ns2='CCCGACCTTAGCACAC'; % LCS is 'TAAGGT' in reverse complement\r\ny_correct = 12/28;\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":112943,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2020-11-28T21:45:20.000Z","updated_at":"2025-10-02T20:10:19.000Z","published_at":"2020-11-28T21:47:59.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular'' chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eRapid DNA sequencing machinary produces short strands of DNA, and these can be arbitrarily orientated - i.e the DNA strand is 'read' from left to right, or right to left (depends on which side is 'grabbed' when reading starts) , and it comes from either the forward or the reverse complement strand that had been uncoiled to facilitate sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHere we are interested in computing the similarity between two strand sequences (called 'reads').\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eWe define the similarity in\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eterms of the length of the longest common subsequence LCS, and lengths of the two sequences, LS1 and LS2 respectively.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSimSeq(S1,S2) = 2*LCS / (LS1+LS2)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eWhen S1 = S2 the similarity score is 1.0\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(also when S1 is equal to S2 reverse complement)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eWhen the sequences are dissimilar the similarity score approaches zero, as well as when one of the sequences is much longer than the other (alternative definitions that correct for length diffrence are possible, but are of no concern here.)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNote that the longest common subsequence LCS can be found in the forward or in the reverse complement direction.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eFor instance, LCS('TACCTGAGA','GACCTGAGC') is equal to 7 since the common substring is 'ACCTGAG' in S1, which matches the reverse complement\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e'ACCTGAG' in S2.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":47513,"title":"DNA Sequence Assembly","description":null,"description_html":"\u003cdiv style = \"text-align: start; line-height: 20.44px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: none solid rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 258px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 406.5px 129px; transform-origin: 406.5px 129px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eDNA fragments are made by DNA sequencer.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eTo find full sequence, we need to concatenate each other using common sequence information.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eSo, when Input sequences are\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(1) ATCGATCGAAGTCATCG\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eGGAAA\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(3)\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e GGAAA\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eGATCGATTACTT\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eCCGAAA\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(2)\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003e CCGAAA\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eACCTAAGGGTTCTCAATGAC .\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eOutput sequence is \u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e'ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC' .\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 20.6667px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 383.5px 10.3333px; text-align: left; transform-origin: 383.5px 10.3333px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function y = your_fcn_name(x)\r\n y = x;\r\nend","test_suite":"%%\r\nx = {'ATCGATCGAAGTCATCGGGAAA'\r\n 'CCGAAAACCTAAGGGTTCTCAATGAC'\r\n 'GGAAAGATCGATTACTTCCGAAA'};\r\ny_correct ='ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC';\r\nassert(isequal(your_fcn_name(x),y_correct))\r\n\r\n\r\n%%\r\nx = {'GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT'\r\n'GGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC'\r\n'AGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG'\r\n'CATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC'\r\n'ATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC'\r\n'CGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC'\r\n'CGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG'\r\n'GTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG'};\r\ny_correct='GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG';\r\nassert(isequal(your_fcn_name(x),y_correct))\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":71768,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2020-11-15T12:55:39.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2020-11-15T12:40:44.000Z","updated_at":"2025-10-02T20:02:57.000Z","published_at":"2020-11-15T12:40:44.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA fragments are made by DNA sequencer.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eTo find full sequence, we need to concatenate each other using common sequence information.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSo, when Input sequences are\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e(1) ATCGATCGAAGTCATCG\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eGGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(3)\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e GGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eGATCGATTACTT\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eCCGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(2)\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003e CCGAAA\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eACCTAAGGGTTCTCAATGAC .\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eOutput sequence is \u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e'ATCGATCGAAGTCATCGGGAAAGATCGATTACTTCCGAAAACCTAAGGGTTCTCAATGAC' .\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":939,"title":"DNA Pattern Match: Performance Metric - Speed","description":"The Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\r\n\r\nAt \u003chttp://imacst.com/issues/volume-3issue-1/ IMACST\u003e the paper \u003chttp://imacst.com/web_documents/1202002.pdf An Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\r\n\r\nMatlab can achieve matching a six pattern set of L=6 in \u003c15 msec (i5/16GB). This is merely a 99.8% time reduction.\r\n\r\n\r\n*Challenge Description:*\r\nDNA is made of letters ACGT, \u003chttp://en.wikipedia.org/wiki/DNA wiki DNA\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\r\n\r\n*Input:* [DNA, DNA_ID, Patterns]\r\n\r\n* DNA is a 1.8M long uint8 row vector of values 0 thru 3.\r\n* DNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\r\n* Patterns is an Nx6 uint8 array where each row corresponds to a search pattern.\r\n\r\n*Output:* Locations\r\n\r\nLocations of all start indices that match any of the patterns\r\n\r\n*Scoring:* Average Time (msec) for a block of L=6 patterns\r\n\r\nExample:\r\n\r\n* DNA= [0 1 2 3 3 2 1 0 1 2 3 3]\r\n* Pattern = [2 3 3 2 1 0]\r\n* Locations = [3]\r\n\r\n*Hints:*\r\n\r\n* Vectorization (Base 4 to Base 10 of 6 character words)\r\n* Bitshift/Reshape to create all words\r\n* Logical Indexing\r\n \r\n\r\nComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza","description_html":"\u003cp\u003eThe Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\u003c/p\u003e\u003cp\u003eAt \u003ca href=\"http://imacst.com/issues/volume-3issue-1/\"\u003eIMACST\u003c/a\u003e the paper \u003ca href=\"http://imacst.com/web_documents/1202002.pdf\"\u003eAn Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003c/a\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\u003c/p\u003e\u003cp\u003eMatlab can achieve matching a six pattern set of L=6 in \u0026lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.\u003c/p\u003e\u003cp\u003e\u003cb\u003eChallenge Description:\u003c/b\u003e\r\nDNA is made of letters ACGT, \u003ca href=\"http://en.wikipedia.org/wiki/DNA\"\u003ewiki DNA\u003c/a\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e [DNA, DNA_ID, Patterns]\u003c/p\u003e\u003cul\u003e\u003cli\u003eDNA is a 1.8M long uint8 row vector of values 0 thru 3.\u003c/li\u003e\u003cli\u003eDNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\u003c/li\u003e\u003cli\u003ePatterns is an Nx6 uint8 array where each row corresponds to a search pattern.\u003c/li\u003e\u003c/ul\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Locations\u003c/p\u003e\u003cp\u003eLocations of all start indices that match any of the patterns\u003c/p\u003e\u003cp\u003e\u003cb\u003eScoring:\u003c/b\u003e Average Time (msec) for a block of L=6 patterns\u003c/p\u003e\u003cp\u003eExample:\u003c/p\u003e\u003cul\u003e\u003cli\u003eDNA= [0 1 2 3 3 2 1 0 1 2 3 3]\u003c/li\u003e\u003cli\u003ePattern = [2 3 3 2 1 0]\u003c/li\u003e\u003cli\u003eLocations = [3]\u003c/li\u003e\u003c/ul\u003e\u003cp\u003e\u003cb\u003eHints:\u003c/b\u003e\u003c/p\u003e\u003cul\u003e\u003cli\u003eVectorization (Base 4 to Base 10 of 6 character words)\u003c/li\u003e\u003cli\u003eBitshift/Reshape to create all words\u003c/li\u003e\u003cli\u003eLogical Indexing\u003c/li\u003e\u003c/ul\u003e\u003cp\u003eComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza\u003c/p\u003e","function_template":"function Locations = find_DNA(DNA, DNA_ID, Patterns)\r\n persistent DNA_ID_loaded % add other DNA created variables\r\n Locations=[];\r\n if isempty(DNA_ID_loaded) || DNA_ID~=DNA_ID_loaded\r\n % Perform initialization actions on DNA vector - optional\r\n DNA_ID_loaded=DNA_ID;\r\n \r\n end % DNA_ID Processing\r\n\r\n\r\n\r\n \r\nend\r\n\r\n\r\n\r\n\r\n","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\n% Functionality Section\r\nPass=1;\r\nw=6;\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=1;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nif isempty(Locations),Pass=0;end\r\nif max(size(Locations))\u003c1024,Pass=0;end\r\nfor i=1:size(Locations,1)\r\n Pass=Pass \u0026\u0026 ismember(DNA(Locations(i,end):Locations(i,end)+w-1),Patterns,'rows');\r\n end\r\n\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,24,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:12,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=2;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nif isempty(Locations),Pass=0;end\r\nif max(size(Locations))\u003c1024,Pass=0;end\r\nfor i=1:size(Locations,1)\r\n Pass=Pass \u0026\u0026 ismember(DNA(Locations(i,end):Locations(i,end)+w-1),Patterns,'rows');\r\n end\r\n\r\n\r\nassert(isequal(Pass,1))\r\n%%\r\n% Timing Section\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=1;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt1=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 1 Time = %i msec\\n',floor(dt1))\r\n\r\n\r\nPatterns=randi(4,24,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:12,:); % Take first 12 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt2=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 2 Time = %i msec\\n',floor(dt2))\r\n\r\n\r\n% New DNA Set\r\nDNA=randi(4,1,1800000,'uint8')-1;\r\nPatterns=randi(4,12,6,'uint8')-1; % Create more than needed\r\nPatterns=unique(Patterns,'rows','stable'); % Elim dupes but maintain random\r\nPatterns=Patterns(1:6,:); % Take first 6 random vectors\r\nPatterns=unique(Patterns,'rows'); % Place in order for easier debugging\r\n\r\nDNA_ID=2;\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\nLocations = find_DNA(DNA, DNA_ID, Patterns);\r\n\r\nt0=clock;\r\nfor i=1:10\r\n Locations = find_DNA(DNA, DNA_ID, Patterns);\r\nend\r\ndt3=etime(clock,t0)*1000; % msec conversion\r\nfprintf('Your Set 3 Time = %i msec\\n',floor(dt3))\r\n\r\n\r\nfeval(@assignin,'caller','score',min(400,floor(double(dt1+dt2+dt3)/30)));\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":9,"test_suite_updated_at":"2012-09-10T03:41:37.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-09-10T00:09:00.000Z","updated_at":"2025-11-21T09:02:33.000Z","published_at":"2012-09-10T03:40:23.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Challenge is to Rapidly find matches of DNA sequences, Length=6, in a 1,800,000 long DNA file.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAt\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://imacst.com/issues/volume-3issue-1/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eIMACST\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e the paper\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://imacst.com/web_documents/1202002.pdf\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAn Intelligent and Efficient Matching Algorithm to Finding a DNA Pattern\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e claimed an astounding time improvement from 9.94 seconds to 7.84 seconds, 21% time reduction, to match six segments of length 6 in a 1.8M long DNA file. Basic probability asserts 1.8M/4^6 * 6 = 2637 matches. The paper's test case produced 2346 matches. The method employed used text processing in C++. The paper's L=25 and L=50 cases will be later challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eMatlab can achieve matching a six pattern set of L=6 in \u0026lt;15 msec (i5/16GB). This is merely a 99.8% time reduction.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eChallenge Description:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e DNA is made of letters ACGT,\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/DNA\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ewiki DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e, which for the purposes of this Matlab Cody Challenge are given values 0 thru 3. (ACGT= 0123)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [DNA, DNA_ID, Patterns]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is a 1.8M long uint8 row vector of values 0 thru 3.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA_ID identifies the DNA segment being processed. Multiple calls using the same DNA_ID will be performed. The first call of a DNA_ID is not timed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003ePatterns is an Nx6 uint8 array where each row corresponds to a search pattern.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Locations\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLocations of all start indices that match any of the patterns\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScoring:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Average Time (msec) for a block of L=6 patterns\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA= [0 1 2 3 3 2 1 0 1 2 3 3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003ePattern = [2 3 3 2 1 0]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLocations = [3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eHints:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eVectorization (Base 4 to Base 10 of 6 character words)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eBitshift/Reshape to create all words\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"1\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLogical Indexing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eComing soon: Genome DNA sequencing of PhagePhix174 and Haempphilus Influenza\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches. \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n ACGTCGGCCATGGACATTACG\r\n ACGTCGGCCAsssssssssss\r\n sssssGGCCATGGACATssss\r\n ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":47658,"title":"Calculate the similarity between DNA sequences ","description":null,"description_html":"\u003cdiv style = \"text-align: start; line-height: 20.44px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: none solid rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 453px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 226.5px; transform-origin: 407px 226.5px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 168px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 84px; text-align: left; transform-origin: 384px 84px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eA DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular'' chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eRapid DNA sequencing machinary produces short strands of DNA, and these can be arbitrarily orientated - i.e the DNA strand is 'read' from left to right, or right to left (depends on which side is 'grabbed' when reading starts) , and it comes from either the forward or the reverse complement strand that had been uncoiled to facilitate sequencing.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eHere we are interested in computing the similarity between two strand sequences (called 'reads').\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWe define the similarity in\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eterms of the length of the longest common subsequence LCS, and lengths of the two sequences, LS1 and LS2 respectively.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eSimSeq(S1,S2) = 2*LCS / (LS1+LS2)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWhen S1 = S2 the similarity score is 1.0\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e(also when S1 is equal to S2 reverse complement)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eWhen the sequences are dissimilar the similarity score approaches zero, as well as when one of the sequences is much longer than the other (alternative definitions that correct for length diffrence are possible, but are of no concern here.)\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eNote that the longest common subsequence LCS can be found in the forward or in the reverse complement direction.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003eFor instance, LCS('TACCTGAGA','GACCTGAGC') is equal to 7 since the common substring is 'ACCTGAG' in S1, which matches the reverse complement\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e'ACCTGAG' in S2.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 0px 0px; transform-origin: 0px 0px; \"\u003e\u003cspan style=\"\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function y = SimSeq(s1,s2)\r\n y=0;\r\nend","test_suite":"s1='TACCTGAGAAGG';\r\ns2='TACCTGAGAAGG';\r\ny_correct = 24/24; % LCS is 'TACCTGAGAAGG' \r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='TACCTGAGAAGG';\r\ns2='CCTTCTCAGGTA';\r\ny_correct = 24/24; % LCS is 'TACCTGAGAAGG' in reverse complement\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='TACCTGAGAAGG';\r\ns2='CCCGACCTGAGCACAC';\r\ny_correct = 14/28; % LCS is 'ACCTGAG' \r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='CCTTCTCAGGTA';\r\ns2='CCCGACCTTAGCACAC'; % LCS is 'CCTT' in forward direction or 'AGGT' in reverse complement\r\ny_correct = 8/28;\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n%%\r\ns1='CCTTAAGGTGTA';\r\ns2='CCCGACCTTAGCACAC'; % LCS is 'TAAGGT' in reverse complement\r\ny_correct = 12/28;\r\nassert(isequal(SimSeq(s1,s2),y_correct))\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":112943,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2020-11-28T21:45:20.000Z","updated_at":"2025-10-02T20:10:19.000Z","published_at":"2020-11-28T21:47:59.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular'' chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eRapid DNA sequencing machinary produces short strands of DNA, and these can be arbitrarily orientated - i.e the DNA strand is 'read' from left to right, or right to left (depends on which side is 'grabbed' when reading starts) , and it comes from either the forward or the reverse complement strand that had been uncoiled to facilitate sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHere we are interested in computing the similarity between two strand sequences (called 'reads').\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eWe define the similarity in\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eterms of the length of the longest common subsequence LCS, and lengths of the two sequences, LS1 and LS2 respectively.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSimSeq(S1,S2) = 2*LCS / (LS1+LS2)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eWhen S1 = S2 the similarity score is 1.0\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e(also when S1 is equal to S2 reverse complement)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eWhen the sequences are dissimilar the similarity score approaches zero, as well as when one of the sequences is much longer than the other (alternative definitions that correct for length diffrence are possible, but are of no concern here.)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNote that the longest common subsequence LCS can be found in the forward or in the reverse complement direction.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003eFor instance, LCS('TACCTGAGA','GACCTGAGC') is equal to 7 since the common substring is 'ACCTGAG' in S1, which matches the reverse complement\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e'ACCTGAG' in S2.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc 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