On Wed, Feb 29, 2012 at 2:05 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Tue, Feb 28, 2012 at 10:31 PM, Dave Clements
<clements@galaxyproject.org> wrote:
> Hi Peter,
>
> I think hmmerscan has been wrapped, but there is a missing "e" in the
> repository name. Look for "hmmscan" in the toolshed. The description for
> it is:
>
> hmmscan, for searching pfam with AA seqs. also included is hmm datatypes
> although hmmbuild, etc. isnt included yetX ill try to finish the rest of the
> hmmer suite soon
>
> Does that help?
>
> Dave C.

Very helpful Dave, thanks.

Actually hmmscan is the name of one of the HMMER binaries, rather than
hmmerscan (with an 'er' in the middle, which was a typo on my part).

I've included Edward directly in this thread hoping he can clarify which
version of HMMER he was wrapping (2 vs 3).

Also I'd like to ask Edward if he could add the word HMMER to the tool's
description to facilitate future searchers (and HMMER2 or HMMER3 as
appropriate).

I might be interested in helping to extend the wrapper for more of the
HMMER3 toolkit. In particular hmmsearch might be relevant, which
is designed for one (or a few) profiles vs. a big seq database while
hmmscan is designed for one (or a few) sequences vs. a big profile
database. See http://selab.janelia.org/people/eddys/blog/?p=424

Regards,

Peter