baselookup

Find nucleotide codes, integers, names, and complements

Syntax

baselookup
baselookup('Complement', SeqNT)
baselookup('Code', CodeValue)
baselookup('Integer', IntegerValue)
baselookup('Name', NameValue)


Arguments

SeqNT	Nucleotide sequence(s) represented by one of the following: Character vector or string containing single-letter codes from the table Nucleotide Lookup Cell array of sequences Two-dimensional character array of sequences Note If the input is multiple sequences, the complement for each sequence is determined independently.
CodeValue	Nucleotide letter code represented by one of the following: Character vector or string specifying a single-letter code representing a nucleotide. For valid single-letter codes, see the table Nucleotide Lookup. Cell array of letter codes. Two-dimensional character array of letter codes.
IntegerValue	Single integer representing a nucleotide. For valid integers, see the table Nucleotide Lookup.
NameValue	Nucleotide name represented by one of the following: Character vector or string specifying a nucleotide name. For valid nucleotide names, see the table Nucleotide Lookup. Cell array of names. Two-dimensional character array of names.

Description

baselookup displays a table of nucleotide codes, integers, names, and complements.

Nucleotide Lookup

Code	Integer	Nucleotide Name	Meaning	Complement
A	1	Adenine	A	T
C	2	Cytosine	C	G
G	3	Guanine	G	C
T	4	Thymine	T	A
U	4	Uracil	U	A
R	5	Purine	A or G	Y
Y	6	Pyrimidine	C or T	R
K	7	Keto	G or T	M
M	8	Amino	A or C	K
S	9	Strong interaction (3 H bonds)	C or G	S
W	10	Weak interaction (2 H bonds)	A or T	W
B	11	Not A	C or G or T	V
D	12	Not C	A or G or T	H
H	13	Not G	A or C or T	D
V	14	Not T or U	A or C or G	B
N, X	15	Any nucleotide	A or C or G or T or U	N
-	16	Gap of indeterminate length	Gap	-

baselookup('Complement', SeqNT) displays the complementary nucleotide sequence.

baselookup('Code', CodeValue) displays the corresponding meaning and nucleotide name. For ambiguous nucleotide codes (R, Y, K, M, S, W, B, D, H, V, N, and X), the nucleotide name is a descriptive name.

baselookup('Integer', IntegerValue) displays the corresponding letter code, meaning, and nucleotide name.

baselookup('Name', NameValue) displays the corresponding letter code, meaning, and nucleotide name or descriptive name.

Examples

Convert a nucleotide sequence to its complementary sequence

baselookup('Complement', 'TAGCTGRCCAAGGCCAAGCGAGCTTN')

ans = 
    'ATCGACYGGTTCCGGTTCGCTCGAAN
     '

Display the meaning and nucleotide name or descriptive name for the nucleotide codes G and Y.

baselookup('Code', 'G')

ans = 
    'G	Guanine
     '

baselookup('Code', 'Y')

ans = 
    'T|C	pYrimidine
     '

Display the nucleotide letter code, meaning, and nucleotide name or descriptive name for the integers 1 and 7.

baselookup('Integer', 1)

ans = 
    'A	A - Adenine
     '

baselookup('Integer', 7)

ans = 
    'K	G|T - Keto
     '

Display the corresponding nucleotide letter code, meaning, and name for cytosine and purine.

baselookup('Name','cytosine')

ans = 
    'C	C - Cytosine
     '

baselookup('Name','purine')

ans = 
    'R	G|A - puRine
     '

Version History

Introduced before R2006a