[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer

Mark Johnson johnsonm at gmail.com
Fri Mar 2 11:15:34 EST 2007


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)?


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