Running Psiblast To Generate Pssms From A Large Number Of Protein Sequences

Question

[cjb60]

Hi there,

I'm working on a project that requires me to generate PSSMs from a very large number of protein sequences (all of these are in .fasta format), however this takes an infeasibly long amount of time with the way I'm doing things at the moment. In general, I'm using this command:

psiblast -db nr -query SOME_PROTEIN_SEQUENCE.fasta -out_ascii_pssm PSSM.txt

And just recently I tried to see if I could speed things up a bit by adding these parameters:

-num_threads 4 -word_size 5

Is there any way to speed up the process in other ways? Or am I out of luck? I'm only interested in generating the PSSMs from these protein sequences and nothing else.

Thanks in advance.

Answer 1

[Pappu]

You can align the sequences and calculate the PSSM by a python script. Take a look at Biopython.