Create Profile Psi-Blast

Question

[Georgia]

I am using version BLAST-2.2.25, how do I generate the profile of all protein sequences that are contained inside an archive query? The command:

blastpgp -d envnr -i envnrfasta -J T -u 1 -j 3 -Q result.asn

but only generates the profile last sequence.

I want the answer of the form: sequence 1: profile 1 sequence 2: Profile 2

[Michael Schubert]

You can't generate a profile (PSSM) from a single sequence, only from a set of sequences. If you do, you only get your underlying substitution matrix out of it. So what exactly is your goal here?

Answer 1

[Chris]

I'm not sure I can follow. What do you mean with 'last sequence' and 'profile' (I guess the PSSM matrix)? In case you have several sequences that you want to blast against your db, simply run the above command for each such sequence alone, i.e. put the single sequence into your query file 'env_nrfasta'. Doing so you get the PSSM matrix for each sequence.

[Georgia]

I have a file with more of the 2.000 sequences, and run this command for each is very costly, my intention is know if have any parameter for read all sequences in file and make another file with all PSSM matrix.

[Daniel Standage]

It is indeed costly to generate PSSMs with psiblast, but you cannot run the command once and yet still get a PSSM for each sequence. Unfortunately, as Chris suggests, it looks like you will have to run psiblast for each individual sequence.