[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer
cjfields at uiuc.edu
Fri Mar 2 11:48:57 EST 2007
On Mar 2, 2007, at 10:15 AM, Mark Johnson wrote:
> On 3/1/07, Chris Fields <cjfields at uiuc.edu> wrote:
> I have been working on an Infernal wrapper (not finished yet but
> getting there) which does this:
> Speaking of Infernal...that's on my shopping list, too. Though we
> don't invoke cmsearch directly, we use the Sanger rfam_scan wrapper
> ( http://www.sanger.ac.uk/Software/Rfam/help/scripts/search/
> rfam_scan.pl), which does a pre-cmsearch blast to determine which
> models to run.
> I wonder whether to wrap the wrapper, or just incorporate the guts
> of rfam_scan into a Bioperl wrapper (if the licensing is compatible)?
You could modify it to use both Bio::Tools::Run::StandAloneBlast and
Bio::Tools::Run::Infernal. I'm still toying with the latter (only
cmsearch works) but will probably get back to it this weekend as I
have a ton of Infernal searches to do.
BTW, the latest Infernal (v0.72, which the wrapper supports) allows
you to prerun a HMM before running with a full-blown CM search and
allows you to specify a bit score cutoff to decrease the noise
level. Much faster, particularly when running full genome searches...
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