Lucio Cetto

Last seen: 2 months ago | Active since 2002

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How to predict unknown data with a RegressionPartitionedSVM-model
Hi, Let me add to what Shubh already said, the partitioned model contains several models, so which one should be used for predi...

4 years ago | 1

Answered
How do you convert a tsv or txt file to a GFF file on matlab, with data you've downloading from NCBI or Ensembl ?
There is a demo function ( |ensemblmart2gff| ) in the toolbox/bioinfo/biodemos directory that may help you to get you started. ...

10 years ago | 0

10 years ago | 0

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Biograph node label elimination. How to?
bg.NodeAutoSize='off' bg.ShowTextInNodes='none' set(bg.Nodes,'Size',[1 1]); set(bg.Nodes,'Shape','circle'); view(b...

10 years ago | 0

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How can I reverse an edge in biograph viewer without redrawing the figure?
You must call the layout engine to redraw graph. This is because in some types of layouts the actual chronological order of the ...

11 years ago | 0

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Saving to BAM files from a BioMap object ?
You can not only split, but you can use this convenient method to filter (or preprocess) your files, for example you can filter ...

11 years ago | 1

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How to open a BAM file?
It may be possible that the BAM file is not ordered. The Bioinfomatics Toolbox (12b) automatically indexes the BAM file, but for...

11 years ago | 0

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dendrograms in clustergram vs pdist->linkage->dendrogram
Clustergram standardizes the data. I am not sure what release you are using but the way you control this option with the input a...

11 years ago | 1

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official examples could not run --- bioinformatics toolbox
This a known issue. There are workarounds already published. <http://www.mathworks.com/support/bugreports/865214> HTH L...

11 years ago | 1

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how to solve Dijkstra algorithm in MATLAB?
I get the distance of 1-16-2-6-10 to be 5.8, while 1-3-6-10 is 5.15. HTH

11 years ago | 0

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msresample error message: The MZ vector is not evenly nor linearly spaced.
Setting the option MISSING to TRUE should only be used when you are certain that the spacing between MZ values follows a linear ...

11 years ago | 0

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Need access to certain fields using BioMap for .bam file reading
Currently, you'll need to look into the mate, wich you could find using the MatePosition. This is not optimal and would require ...

12 years ago | 0

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Bioinformatics toolbox - featuresmap question
Razvan: featuresmap cannot do what you need, you'll need to plot the CDS manually, hopefully this gets you started: figu...

12 years ago | 0

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open huge SAM files
The 4GB limitation for BioIndexedFile (which is the back-end support to read SAM files into BioMap) has been removed in 12a. Bef...

12 years ago | 0

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HeatMap to Figure in 2009b vs. 2010b
This is a bug in 2010b, this was later fixed. This has a simple workaround, use: plot(hmo,figure('Renderer','ZBuffer','Vi...

12 years ago | 0

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FASTA AND BLAST
None of these alignment algorithms are included in Matlab. Do not mix the "fasta" alignment algorithm with the "fasta" file ...

12 years ago | 1

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why nucleotides is more than 4?
Ambiguous nucleotide symbols are used to characterize sequences that can have variations. It was introduced in the 80's and they...

12 years ago | 1

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Sort items to existing cluster groups
Use the function |cluster| to give a cluster idx to each sample in X: C = cluster(Z,'MaxClust',number_of_groups); Then f...

12 years ago | 0

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Dot plot screen resolution
You could visualize the dot plot by regions: seqdotplot(AHSINS5H5N1(1:500),AHSINS5H5N1(1:500),11,7) seqdotplot(AHSINS5H5N1...

12 years ago | 0

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tie-breaking in nwalign
Under ties, the simplegap algorithm favors first diagonal (matches/missmatches) then gap instertions in the first sequence and...

12 years ago | 0

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Difference between heatmap and clustermap
clustergram automatically standarizes the data in order to maximize the usage of the colormap. You may also alter the dynamic ra...

12 years ago | 0

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Load files to ngsbrowser from command line
This is undocummented, unfortunately it is only possible for short read data: bm1 = BioMap('mysamfile.sam') bm2 = BioMap...

12 years ago | 1

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Sequence Distance
When you are comparing sequences it is common to first align them using a dynamic programing algorithm. SEQPDIST uses NWALIGN to...

13 years ago | 0

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Bioinformatics
The first input of multialign is a collection of sequences to be aligned, this can be: 1) an array of structures with the "Seq...

13 years ago | 2

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Colorbar displays in new figure
Adding to what Patrick said, please not that you can pass a PVP to the constructor HeatMap object with the colormap: HeatMap(...

13 years ago | 0

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Error message when use geosoftread() function
In 2008a GEOSOFTREAD was only able to read data sets GDS and sample GSM files. Is your file a GSE file? You should use instead G...

13 years ago | 0

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How to understand "predecessor node" of the winning paths?
The PRED in your example 'encodes' all shortest paths from S to all other nodes, for example the shortest path between 1 and 6 i...

13 years ago | 1

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Problem with biograph layout
The layout engine will readjust the size of the page according with the positions of the nodes, so, if you are going to set the ...

13 years ago | 2

Lucio Cetto

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