[Bioperl-l] Review request: Merged hmmer2/3 parser

Kai Blin kai.blin at biotech.uni-tuebingen.de
Fri Nov 5 08:56:23 EDT 2010


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On 2010-11-05 13:35, Dave Messina wrote:
> I may have missed some recent off-list discussion, but I thought we
> explicitly talked about *not* merging these since it will complicate
> future maintenance and Hmmer2 will be obsolete in the near future.

Yes, that's what I thought until about last week. Then I was bitten by
the fact that Hmmer3 can't do global alignments, so you can't reliably
use Hmmer3 to extract protein domains using the domain's motif. As this
seems to be a common use case, I think we'll end up supporting hmmer2
for quite a while now.

There's currently no plans by the Hmmer authors to add globlal and
glocal (whole profile alignments against parts of the sequence)
alignments to hmmer3. They suggested to keep using hmmer2 for now.

For this reason I decided to try and merge the two parsers to a point
where users don't have to care which version of hmmer their file is.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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