[Biojava-l] Reading pfam/Stockholm format

[Simon Brocklehurst]

Thomas Down wrote:

> No, I don't think any of our current SeqIO code will handle
> this format.  Certainly, I'm amazed that the EmblLikeFormat
> got as far as it did -- STOCKHOLM format really isn't much
> like EMBL at all (even in the headers, there's the
> extra #=<tag> stuff, to be confusing).
>
> I don't know much about the HMMer alignment parser, but
> a quick look suggests that it's designed to parse a rather
> different format.  Simon?

You're right, the BlastLikeSAXParser parser deals with the output from hmmer
programs.

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