How to calculate PSSM for large batch of proteins?

Question

[aakashy01]

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?

[Arsenal]

Can you try psiblast standalone it in a high-performance computing environment?

[aakashy01]

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.