[Biojava-l] Blast and PDB

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Tue, 15 Aug 2000 19:53:49 +0100

Thomas Down wrote:

> Hi...
> I've just finished checking in the new Blast and PDB
> parsing code submitted by Simon Brocklehurst, Tim Dilks,
> Colin Hardman, and Stuart Johnston, all of Cambridge
> Antibody Technology.  Take a look at the code in
> org.biojava.bio.program.

Many thanks again for taking the time to import the source into the CVS.

Just so people know what to expect next from CAT... here's what's in the

On the Blast-like front:

o Better support for HMMER
o XSLT transforms for HTML visualisation of results
o Bug-fixes - there is now enough functionality in this new parsing
framework that we can contemplate replacing our existing Blast parsers
in real systems.  I would be surprised if we don't come across some
issues using this for real.
o Tidying up the guts of the code, some of the code isn't there
particularly nice.

Over the next month, it would be good to get to the point where we tie
down element names etc., so that they're stable.  In other words, the
next month is the time to try out the code, and flag up things you
really hate etc.!

On the macromolecular structure front:

o Much more complete parsing of PDB files
o Some fairly sophisticated Java object models of macromolecular
o Java3D macromolecular structure visualisation (which has one or two
quite nice features that I won't go into now)
o Some Java structure analysis algorithms

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