[Biojava-l] status? Blast parser?

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Wed, 16 Feb 2000 19:07:13 +0000

> We've already decided upon a meta-data convention for BLAST content.  My
> feeling is that you'll run into trouble if you try to have 1 standard for
> all similarity algorithms, and you'll be better off creating a standard
> specifically for each algorithm, and then a more general one that they can
> map into.

I wouldn't dream of suggesting a single standard for all similarity algorithms.  I
was merely suggesting that where you can identify similarities between one
programming effort and another, you will benefit in terms of productivity from
reusing code.  The reality is that outputs from BLAST and HMMER really do look
pretty similar at the moment.  We currently use a lot of the same code to parse
the output from both pieces of software.

Absolutley no reason why this has to be the case in the future though.

I'm open to suggestion here - if people want to use biopython conventions for
metadata, that's what we'll do.  What about the bioxml proposal on BLAST XML
element naming from the guys at SB? Is this similar to the biopython stuff?

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