Blastpgp_Mutant_Residue
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.
• 2,977 views
•
link
updated
by
Chris •
•
written
by
kylejudita •
•
written
by
kylejudita •
1 answer
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.
Log in to answer this question.
More posts like this
-
MFE in RNA structure
written by Ebtihal •
-
Comparing GSEA mutant data to wild type
written by conmul •
-
Performing Needleman-Wunsch Global Alignment for multiple mutant proteins against wild-type
written by VolEr •
-
list variants from concatonate snp alignment
written by samuel.lipworth •
-
Trajectory File of MD
written by naeem.mahmood •
-
Features I Can Extract To Find Mutation Impact On Protein Stability
written by kylejudita •
-
Looking For Features To Predict Mutation Impacts
written by kylejudita •
-
Prediction Of Mutation Impact
written by kylejudita •
-
Protein Sequence Alignment
written by kylejudita •
-
Psi-Blast Alignments
written by kylejudita •
(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.