[Biojava-l] status? Blast parser?

[Simon Brocklehurst]

Dear All,

Having previously posted that CAT wouldn't be contributing to biojava,
I'm happy to say that we now have the OK to contribute code that we
regard as precompetetive.  Parsers for things like Blast and Hmmer
certainly fall into that category.


We'd be happy contribute this functionality to biojava (our systems
extract essentially all the information from the output of these type of
common bioinformatics software).  Before we release any code, however ,
I'd like to see some feedback on the list about:

a) Do people actually want parsers for Blast, Hmmer etc?

If the answer is yes:

b) What do people want to use them for - we'd like to make them work out
of the box for people if possible.  What we could go with pretty much
right away (subject to finding the time to package it all up in a
suitable form for biojava) are classes for getting all the information
out that you can use in your own systems, and classes designed to
produce marked up HTML etc.

It would be good to have some use cases from people out there (Jared?)

Simon
--
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