Generate Psi-Blast Profile

Question

[Daniel Standage]

I am reading this paper on protein fold classification and am particularly interested in their formulation of the profile-based composition vector (PCV). I downloaded an arbitrary set of proteins from PDB, hoping that I could construct a PCV for one of the proteins in that set.

Given a query protein sequence query.faa and a database of protein sequences db.faa, how can I generate a PSI-BLAST profile for query.faa? I have looked at the help statement for the psiblast program distributed with NCBI BLAST+ 2.2.25, but I don't see any relevant options.

Answer 1

[Rm]

To Output PSI-BLAST Matrix File (PSSM) in ASCII use:

1. Older blast versions use "blastpgp -Q pssm_matrix_file -j 2" i.e. with minimum of two iterations.

2. with current version of blast (blast+) use -out_ascii_pssm and -num_iterations 2 options.

for example:

psiblast -db pdbaa -out_pssm my_protein.ckp -evalue 0.01 -query my_protein -out_ascii_pssm ascii_mtx_file -out output_file -num_iterations 3

For generating PSSM to "use for the searches" option will be "-out_pssm"

[Daniel Standage]

I had originally tried the -out_ascii_pssm option for psiblast program, but no profile file wasn't created. I wasn't sure if PSSM and profile were referring to the same thing.

[Rm]

i just tried this it worked: psiblast -db pdbaa -out_pssm my_protein.ckp -evalue 0.01 -query my_protein -out_ascii_pssm ascii_mtx_file -out output_file -num_iterations 3

[Rm]

i think "-num_iterations" has to be 2 or more... (i haven't tested it though)

[Daniel Standage]

Ahh, I did not set the -num_iterations option. I'll give that a shot.

[Daniel Standage]

It worked! If you edit your answer to include a summary of your comments, I will accept it as the correct answer.

[shane.neeley]

How do I get one of the older versions?

[Rm]

if ask a new question: open it as new, not as a comment: anyways check here: ftp://ftp.ncbi.nih.gov/blast/executables/release/

[shane.neeley]

Ok opened a new question. Thank you.