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PSSM format for command-line PSIBLAST
Entering edit mode
14 months ago
eroljb • 0

I am trying to run PSI-BLAST from the command line, but keep getting the following error: BLAST query/options error: Unsupported format for PSSM

I am getting the PSSM by downloading it from this page:

I already created a protein sequence database with makeblastdb, and I think the problem is in the PSSM. I just cant find enough information on this.

Any help would be appreciated. Thanks in advance.

Entering edit mode
15 months ago
fishgolden • 390

I think you have an ascii pssm file.

I think psi-blast accepts only asn.1 format file as pssm which is non-human-friendly format.

The asn.1 format files can be downloaded from cdd FTP site as cdd.tar.gz .

BUUUUUT using that pssm, I got an error as follows (I tried just now).

BLAST engine error: PSSM has a scaling factor of 100. PSI-BLAST does not accept scaled PSSMs

If your goal is finding the distant homolog, I recommend you to download msa of the domain which can be found in the same FTP site.

And submit it to hmmsearch (it may misunderstand multiple fasta with other format. thus it's better to convert fasta to stockholm format ).

Because it is said that the performance of psi-blast search with -in_msa option is significiantly lower than that of using PSSM.


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