[Biojava-l] Preparation for a 1.1 release?

[Simon Brocklehurst]

uwe.plikat@pharma.Novartis.com wrote:

> Hi Thomas,
>
> reading "Blast parsers" and hearing Matthews presentation last week at EBI,
> I just want to make one comment:
> Matthew mentioned a Blast2XML parser. Since Blast by itself can produce XML
> output (option -m7) it would be a good idea, if this parser (kind of
> obsolete...) produces the XML format identical to the original one from
> NCBI. The DTD is available at NCBI's ftp site.

Hi Uwe,

One of the points of the XML format for the biojava Blast-like stuff is that it
doesn't actually revolve around NCBI Blast.  That is, it can represent data
output from WU-Blast and Hmmer as well.  The biojava XML format is also
designed to be invariant with respect to different versions of all these
programs (once it goes into a full biojava release).  I think it remains to be
seen whether or not the NCBI DTD remains stable, or is subject to change
without notice or reference to users in upcoming versions of Blast.

I don't think we have yet put enough code into biojava yet, to demonstrate the
utility of taking this approach.  Having said all that, we are hoping to make
everything work smoothly and seamlessly with the NCBI Blast XML output.

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