How to calculate PSSM matrix for a protein?
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17 months ago
Misha ▴ 50

Hello,

How to generate PSSM for a protein sequence to form a feature vector using a window size technique in order to use it for machine learning purposes?

Thank you.

PSSM Feature-Vector Protein-Sequence • 730 views
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Entering edit mode
17 months ago
Mensur Dlakic ★ 14k

A simple way of doing that is to install BLAST locally, and run something like the following command:

psiblast -query protein.fas -db nr -num_iterations 3 -out_ascii_pssm protein.pssm

If you never ran BLAST locally, there is a detailed tutorial here.

In case you learn best by example, you may want to check out how the whole procedure is done by Porter5, in scripts directory.

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Hi, Thanks a lot for the information. I will surely work on it.

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