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