Am I correctly running psiblast (using a PSSM as query)?

Question

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Hello,

I am attempting to execute psiblast using multiple PSSMs as queries against a protein database of a specific strain. I previously conducted a blastP and found some results for my proteins of interest, but they were limited. Therefore, I thought that running a PSIBLAST might yield more results. I generated some PSSMs for these proteins and then ran psiblast, but all the outputs are empty.

psiblast -query pssm.smp -evalue 1e-5 -db '/db/strain_protein.db'  -outfmt \"6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp\" -num_threads 15 -out ./output/test2.tsv -num_iterations 1 -save_pssm_after_last_round -out_pssm ./PSSM/test2.smp

I suspect that I might be running the wrong command because I received this Console Log

I posted the console log on Pastebin due to its length.

Answer 1

[Mensur Dlakic]

The -query switch is meant for FASTA sequences, which is not what you have. The easiest way to figure this out, and that goes for any program, is to run it in the help mode and read carefully through the options. If you type psiblast -help they will be displayed on the screen. I haven't ran psiblast in a long time, but most likely you should replace -query with -in_pssm.