hi, peter - i will fix the description and upload hmmsearch and infernal today. On Wed, Feb 29, 2012 at 2:05 AM, Peter Cock <p.j.a.cock@googlemail.com>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
On Tue, Feb 28, 2012 at 10:31 PM, Dave Clements <clements@galaxyproject.org> wrote: 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