[Biojava-l] Reading pfam/Stockholm format

[Thomas Down]

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?

I think there's some kind of support for this in BioPerl,
but I couldn't say for sure.

    Thomas.



On Wed, Sep 12, 2001 at 09:25:40AM -0500, Michael Muratet wrote:
> Greetings All:
> 
> I've been trying to read pfam files to get the protein accessions for
> each family. This almost works using Embl format readers, but the
> (Stockholm) sequence format in the fifth or sixth family is causing an
> exception:
> 
> I can't see anything in the API that says it supports the Stockholm
> format per se, although there appear to be some hmmr related classes
> that might work. Does anybody have any suggestions? Is there some other
> tool set I should investigate (the WashU tools, or bioperl, etc.)?