[Biojava-l] status? Blast parser?

[Simon Brocklehurst]

"Triplett, Terry" wrote:

> Over the short term being able to get at the information for reports or
> further analysis, and the ability to dump HTML (with some control over
> format/layout) would be great.  That allows prototypes and simple apps to be
> created with a minimum of fuss - with timelines being what they are, simple
> and quick is important.  Over the long term, the scenario that Matthew
> described sounds really compelling and it would definitely be nice to see
> things move in that direction.

It's not hard to add SAX functionality to our systems, and if the consensus view
of people on the list is that we should go ahead and use CAT's code as the basis
for the biojava BLAST parser, we will definitely implement that fairly quickly.
If we get to that point, we'll need to agree on some standard meta data
conventions and I'll post a proposal (e.g. we are keen for this software to work
with software that has generic BLAST-like output (e.g. HMMER) with the minimum
of effort, so our proposal would probably reflect that).

With respect to your comment "with some control over format/layout", can you be
more specific as to what you mean by that?

Simon

--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com