Protein Sequence Alignment

Question

[kylejudita]

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.

[Neilfws]

This question is almost a duplicate of your previous: http://www.biostars.org/post/show/48569/psi-blast-alignments/.

Answer 1

[Istvan Albert]

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.

Answer 2

[samsara]

I think, you need to use BioJava. Check this post. Could be helpful.