MATLAB: What are the differences in using the Bioinfomatics Toolbox 2.1 on a Macintosh versus a Windows machine

affyaffyreadbioinfomaticsBioinformatics Toolboxmactoolbox

I would like to know what the differences are in using the Bioinfomatics Toolbox on a Mac versus a Windows machine.

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The AFFYREAD function is not supported on the Mac. Also the DDE and COM interface options are only available on Windows machines. The size of a data set should not significantly affect how the Bioinfomatics Toolbox works on one operating system versus another.

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MATLAB: Does the Bioinformatics Toolbox support Selenocysteine

This error occurs since the Bioinformatics Toolbox does not support the amino acid Selenocysteine with symbol 'U'. Hence NWALIGN fails.

The problem with alignment is that none of the standard scoring matrices for alignment include Selenocysteine. One possible workaround is to convert U to X (the symbol for 'any' amino acid) and then the alignment will not error out.

A code similar to the following can be used to avoid the error:

Seq1 =  'uarndcqeghilkumfpstwyv';
Seq2 =  'auurndcqeghilkmufpstwyv';
Seq1_X = strrep(Seq1,'u','x');
Seq2_X = strrep(Seq2,'u','x');
[score,alignment] = nwalign(Seq1_X,Seq2_X);
alignment = reshape(strrep(alignment(:)','X','U'),size(alignment));

MATLAB: Bioinfomatics toolbox hardware optmization

The Bioinformatics Toolbox does not have any native alignment functions; for now it relies on Bowtie2, which is available as a support package. To my knowledge Bowtie2 is not optimized to run on GPUs. None of the Bioinformatics Toolbox functions have been tested with or optimized for gpuArrays, but some may benefit from optimizations on the native data types like double.

However, bowtie2 does support multiple threads, and does not have particularly high memory requirement, so 16GB should be enough.

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Related Solutions

MATLAB: Does the Bioinformatics Toolbox support Selenocysteine

MATLAB: Bioinfomatics toolbox hardware optmization

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