PSSM format for command-line PSIBLAST

Question

[eroljb]

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: https://www.ncbi.nlm.nih.gov/Class/Structure/pssm/pssm_viewer.cgi?mode=Position&cd=cd00209.

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.

Answer 1

[fishgolden]

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 ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/ 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.

ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/fasta.tar.gz

And submit it to hmmsearch (it may misunderstand multiple fasta with other format. thus it's better to convert fasta to stockholm format ). https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch

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