[Bioperl-l] bioperl-hmmer3 question

Kai Blin kai.blin at biotech.uni-tuebingen.de
Wed Nov 24 01:24:22 EST 2010

On 2010-11-23 00:41, Evan Staton wrote:

Hi Evan,

> Everything works with the latest release of bioperl-live. My bioperl was
> 1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
> did not realize it had been incorporated into the latest distribution). All
> the tests passed and all the routines worked before except for the
> $hsp->query_string and $hsp->hit_string, but that is resolved now.

I recently fixed this in bioperl-live when I bumped into that feature
missing. I didn't bother to update the bioperl-hmmer3 repository.
Perhaps it should be deleted to avoid the confusion.

Also, in bioperl-live, the Bio::SearchIO::hmmer parser now supports
hmmer2 and hmmer3 parsing, but by all means go for the specific parser
class if you know the version of hmmer result you're loading. :)

On a side note, even though you're probably aware of this... HMMer3 only
does local alignments, so it's not really good for domain extraction. It
is very fast, but if your software uses a profile based search to
extract specific amino acid motifs HMMer3 might let you down.
Just as a caveat that has bitten me recently.


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

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