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Psi-Blast Alignments

  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

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updated by Gabriel R. Gabriel R. • written by kylejudita • kylejudita

1 answer

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.

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written by Gabriel R. Gabriel R.

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