I've encountered a problem when generating PSSM from multiple-sequence query with PSI-BLAST. I want to have a query with single PSSM output for each sequence, or at least a big-single file with every sequence's PSSM output in there.
If it's single sequence query, it would be easy
If it's a multiple sequence query, only the last sequence in the fasta input will be printed the PSSM file. Even though the overall PSI-BLAST output provided all sequence output, with iterations as I specified.
Is there anyway for me to solve this?
EDITTED: I've thought about the idea of running each sequence in a seperate fasta file. But in my case I think it's hard, because if I do so, I need to submit about 15 thousand jobs to my college server, which cost so much resources and affect others' jobs. (end of editted)
My command is something like this:
psiblast -query ./a_multiple_seq_test.fasta -db nr -num_iterations 2 -out_ascii_pssm pssm.chk
Thanks in advance. Any suggestion will be highly appreciated