convert FASTA format file of amino acids sequen to High diemntionl vetors
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6.6 years ago
safaa2comp • 0

how to prepare amino acids sequence (FASTA) format file to a form of matrix, that help me to classify the sequence. I read in some papers they get PSI_BLAST profile of 20* N vector, OR 20*(2W+1) where W refer to the number of neighborhood and 2 refer to the left and right sides and 1 refer to the residue itself , this mean if w =7 then it represent the residue and the 7 left neighbors and 7 right neighbors ? how could i do this?

Thanks

blast pssm sequence FASTA HMMs • 2.4k views
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Wow. This is a loaded question. First, why would you want to do this, what are you expecting to gain as a final result? Second, why not use PSI-BLAST if distantly related sequences is what you are looking for? Why does it need to be a "HD vector"? If you are looking for a close neighbourhood, why not use a clustering algorithm like kclust or cd-hit? as I said, a loaded question that requires a bit more elaboration.

cheers

mxs

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