Psi-Blast Alignments

Question

[kylejudita]

1. I want to pass a protein sequence using java code to find the relative frequency of wildtype residue in PSI-BLAST alignments

2. Also I would like to know how to get relative frequency of mutant residue in PSI-BLAST alignments

3. How to get PSI-BLAST PSSM for wildtype residue and mutant type

I use java code

Answer 1

[Gabriel R.]

PSI-BLAST will only give you a multiple sequence alignment with various homologous proteins. I assume you work with various individuals from the same species. I would just look at columns where there are no indels nearby in the alignment and get the frequency of the amino acids on a per column basis. Which one is mutant or wildtype is very much up to interpretation.