Question: Protein Sequence Alignment
0
gravatar for kylejudita
5.2 years ago by
kylejudita90
kylejudita90 wrote:

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.

pssm blast • 1.3k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 5.2 years ago by kylejudita90

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

ADD REPLYlink written 5.2 years ago by Neilfws47k
1
gravatar for Istvan Albert
5.2 years ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k wrote:

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.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Istvan Albert ♦♦ 73k
0
gravatar for samsara
5.2 years ago by
samsara510
The Earth
samsara510 wrote:

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

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by samsara510
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