How to retrieve psi blast pssm for each sequence in my query

Question

[Muny]

Hello everyone, I have a fasta file containing several protein sequences and I want to construct a PSSM for each sequence for downstream analysis. The idea is to run three iterations of psi blast against my reference database and use the resulting pssm for feature extraction in programs like POSSUM. The problem I am encountering is after successfully runingn the blast using the following command:

psiblast -db uniref50/uniref50.fasta -query fasta/query.fasta -out_pssm pssm.matrix -num_iterations 3

When I query the file query.fasta which contains multiple sequences, the result is a pssm file that contains the matrix for only a single sequence. What am I doing wrong? Is there a different method I should be using to generate PSSM profiles for all of my query sequences? I apologize if this is a simple solution, after several hours of search I have not been able to find much documentation for this specific problem.

Answer 1

[Mensur Dlakic]

You can't make multiple PSSM profiles that way. Since you are giving a single profile name, the program goes through each sequence and over-writes the profile.

The only way I know how to do this is to separate your group of sequences into individual FASTA files, then run this command while specifying different PSSM profile names.

[Muny]

Okay I can do that, thank you so much for your response.