Question: Generate Psi-Blast Profile
1
gravatar for Daniel Standage
8.7 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

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.

classification protein • 6.2k views
ADD COMMENTlink written 8.7 years ago by Daniel Standage3.9k
2
gravatar for Rm
8.7 years ago by
Rm8.0k
Danville, PA
Rm8.0k wrote:

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"

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Rm8.0k

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.

ADD REPLYlink written 8.7 years ago by Daniel Standage3.9k

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

ADD REPLYlink written 8.7 years ago by Rm8.0k

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

ADD REPLYlink written 8.7 years ago by Rm8.0k

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

ADD REPLYlink written 8.7 years ago by Daniel Standage3.9k

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

ADD REPLYlink written 8.7 years ago by Daniel Standage3.9k

How do I get one of the older versions?

ADD REPLYlink written 7.8 years ago by shane.neeley50

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

ADD REPLYlink written 7.8 years ago by Rm8.0k

Ok opened a new question. Thank you.

ADD REPLYlink written 7.8 years ago by shane.neeley50
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