I want to know how to call Blast from java code, I have wildtype residue, mutant residue, position of mutation, and protein sequence
I want to calculate the frequency of wildtype residue, mutant residue, PSSM, PISC conservation score for wildtype and mutant residues.
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written
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kylejudita •
2 answers
You would call blast in the same way you would call any other external program. If you don't know how that is supposed to work you will need to ask on a programming forum such as StackOverflow
If you want to do bioinformatics programming with java you ought to look at BioJava. The real challenge is not as much about running blast in an automated way (for that you don't need java, you can do it from a shell script) but parsing and interpreting the results. The BioJava Cookbook entries on blast might help.
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Electrostatic free energy of folding for protein (residue wise)
written by geek_bio •
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Determination of conservative residues via Conservation Code
written by shilyaev.n.g •
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Residue Conservation: Sequence Logo Vs Codeml Or Rate4Site
written by Pappu
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Features I Can Extract To Find Mutation Impact On Protein Stability
written by kylejudita •
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Looking For Features To Predict Mutation Impacts
written by kylejudita •
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Prediction Of Mutation Impact
written by kylejudita •
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Blastpgp_Mutant_Residue
written by kylejudita •
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Psi-Blast Alignments
written by kylejudita •
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Calculating Conservation Score From Mutiple Sequence Alignment
written by Hari •
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Conservation Score Of Amino Acid Positions In Human Proteins
written by Khader Shameer
This question is almost a duplicate of your previous: http://www.biostars.org/post/show/48569/psi-blast-alignments/.