[Biojava-l] Blast And Biojava

[Thomas Down]

On Tue, Feb 12, 2002 at 01:44:34PM -0500, Ratiba Terbaoui wrote:
> 
> hello,
> 
> I'm a new user of Biojava and i want to know if i can run Blast using
> Biojava, which classes i have tu use

Hi...

BioJava includes some a fairly advanced parser for output
from the `blast' family of programs.  There's some tutorial
documentation about this on the website:

   http://www.biojava.org/tutorials/blastlikeParsingCookBook/cookbook.html

You might also like to look at the javadoc documentation
for the packages:

  org.biojava.bio.program.sax
  org.biojava.bio.program.ssbind

What this code /doesn't/ do for you is run the blast program
itself.  At the moment, the best way to do this is to use
the Java Process API.  Look at the classes java.lang.Runtime
and java.lang.Process in the Java API.

It might be nice to have a wrapper within BioJava for
launching blast, but this potentially leads to awkward
questions, like where to find blast executables, how to
set command line options, etc...

Hope you find this a good starting point -- mail me or
the list if you have any trouble,

    Thomas.