Hi, I wonder how I can use mutant residue or wild type residue and position with blastpgp. Does it have parameters to accept any of these.
What is it you want to achieve? A common scenario is: Given a protein sequence and a mutation in the form wtposmt (e.g. M1D), what are the PSSM values for M and D at position 1? To answer that question you have to psi-blast your sequence against a sequence database and parse the PSSM matrix for those two values. There is no blast option that does all of this for you.
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version 2.3.6
(1) This question is very unclear, try to be more specific; (2) documentation for blastpgp, including its parameters, is widely available on the Web; (3) blastpgp is an old BLAST program, now considered by NCBI as "legacy" (i.e. use something newer). If you mean - how to use mutated sequences as BLAST queries - the answer is: edit the sequence before submission.
Hi, kindly, what is the newer version of blastpgp, as you mentioned is is considered legacy. Basically what am trying to do is to find some features from the original sequence and the mutated one as I want to "predict the mutation impact on protein function"
The executable for the newer version is named psiblast, part of the BLAST+ package. See http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download for more information.