[Biojava-l] Blast

[Thomas Down]

On Tue, Nov 06, 2001 at 04:02:53AM -0800, SAMEER MOHTA wrote:
> Hi All,
> 
> Can we fire a Blast search using BioJava (without
> using Blast client). If so then what all packaes are
> used for the same and what is the procedure.
> I suppose this facility is available in BioPerl. But i
> want to know is there any way in BioJava.

BioJava has a good solid parser for blast output, but not
currently any way of launching the blast program itself.  I
think the expectation is that you would do that yourself
using Java process objects, or possibly talk across the network
to some kind of blast server.

I can see the advantages of having some kind of blast-launching
shortcut system.  The trouble with this is that there are lots of
variables: path to executable, which version you're using, which
options to support, etc., etc.

We should look at what Bioperl do for this.

> other thing, is there any facility in BioJava to parse
> OMIM data.

Not yet.  Would be nice to have, though :-)

   Thomas.