[Biojava-l] status? Blast parser?

[Simon Brocklehurst]

Jared Nedzel wrote:

> Simon:
>
> Sorry for the delayed response.  Yes, I want a Blast parser.
> I want to be able to give the parser a Blast output file.
> I want to be able to get:
>
>   - all the hits
>   - the best hit
>
> For each hit, get the set of consistent HSPs. For the hsps,
> get the P and E values and the bases, the ranges (query and
> subject), the gaps, etc.
>
> At this point, I don't need or want html or xml.  Instead,
> I want objects (hits, hsps, etc.).

Thanks for that Jared - we can deal with that easily enough.  Expect something
to be available to play with soon (next week I hope).

--
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