[Biojava-l] sequence similarity searches - some code

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Thu, 29 Jun 2000 20:44:39 +0100

Gerald Loeffler wrote:

> hi!
> Since the topic of BLAST-parsing was mentioned again in an earlier mail,
> i thought i could share with you an object-model for sequence-similarity
> searches that i've developed over the last few days.

Dear All,

Speaking of which, I have available a *very* pre-release version available of the Blast-like SAX parser
we'll be submitting to biojava (SAX events according to the DTD I put up a while back on the list).
Anyone who needs this urgently please e-mail me, and I'll send a tar.gz file.  I say urgently because
the code is a mess at the moment, a few things hardcoded in that shouldn't be - these will obviously be
removed in the full release.

All that's included in this pre-release is a mechanism to generate SAX events from native Blast
output.  That is I haven't included any interesting XML DocumentHandlers - except a trivial one that
makes an XML document from native output.

Estimated time to submit initial full release to biojava is currently two weeks. This should include
support for more blast-like software, and interesting XML DocumentHandlers, and HTML rendering.

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK