[Bioperl-l] Bio::Tools::Glimmer for glimmer2/3

Chris Fields cjfields at uiuc.edu
Tue Dec 19 14:31:17 EST 2006


On Dec 19, 2006, at 12:49 PM, Andrew Stewart wrote:

> I see that Bio::Tools::Glimmer documentation clearly states that this
> module is intended for use with GlimmerM (eukaryotic version) only.
> I am wondering if anyone can recall any talk about adopting
> Bio::Tools::Glimmer for Glimmer2 / Glimmer3 (prokaryotic version)?
> I've searched the list history with little luck other than someone
> else  asking a similar question.

There is a thread here:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12546/ 
focus=12546

> If not, does anyone have any thoughts on how difficult it might be to
> implement support for glimmer2/3 result parsing?  Perhaps just a
> matter of editing the _parse_predictions method?

It depends on how different the various Glimmer formats are; I'll  
have to look at the ones Torsten added in CVS.  You could always try  
modifying Bio::Tools::Glimmer to parse Glimmer2/3 and GlimmerM  
reports, but based on the mail list thread above it may not be so  
straightforward.

chris




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