How to calculate PSSM for large batch of proteins?
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4 months ago
aakashy01 • 0

I tried to use local psiblast but ran out of memory, and also tried 'https://webs.iiitd.edu.in/raghava/pfeature/pssm_profile1.php', but it gave many missing values for several residues for a protein, so is there another way to calculate pssm for large batch of protein sequences?

PSIBLAST BLAST PSSM MACHINELEARNING • 222 views
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Can you try psiblast standalone it in a high-performance computing environment?

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Hello, sorry for my late reply and thanks for your reply, actually, i don't have access to high performance computing environment, but i came across this code 'https://github.com/MsAlEhR/bio-protein-fold-recognition/blob/master/src/pssm_clc.py' which uses biopython but i am facing a problem in it, that when we download xml file of a protein only one iteration of blastp is carried out , but i think for pssm atleast three iterations should be there.

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