[Biojava-l] Blast-like SAX parser - HMMER support

[Simon Brocklehurst]

Dear All,

We've finally got around to adding pretty full support for parsing HMMER
output in the BlastLikeSAXParser.  Specifically, HmmerSearch and
HmmerPfam.  It should just work out of the box - i.e. you throw HMMER
output at the BlastLikeSAXParser, and it should deal with it.

As a consequence, we've made some minor changes to the DTD relating to
dealing properly with hmmer output.  Whilst we were doing this, we also
incorporated:

o Keith's suggestions on the list (with one minor difference discussed
off-line).
o Added a bitScore attribute (from a request at the last biojava
bootcamp) (the blast parsers don't report this yet, but they will...)

We don't think the changes to the DTD break anything that has gone
before - shout if they do.

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