[Bioperl-l] Bio::Tools::Glimmer

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Tue Sep 19 19:44:45 EDT 2006


Mark,

>     The initial checkin comments (circa '03) for Bio::Tools::Glimmer
> describe it as a 'GlimmerM 3.0' parser.  The POD says '...a module for
> parsing Glimmer predictions (currently GlimmerM
> 3.0 is all that has been tested)...'.  However, the latest version of
> GlimmerM looks to be 2.5.1 (ftp://ftp.tigr.org/pub/software/GlimmerM),
> and there are multiple versions/flavors of Glimmer besides GlimmerM:
> 
> Glimmer 2.X ( bacteria, archaea, and viruses):
>     http://www.cbcb.umd.edu/software/glimmer/glimmer2.jun01.shtml
> Glimmer 3.X ( bacteria, archaea, and viruses):
>     http://www.cbcb.umd.edu/software/glimmer/
> GlimmerHMM ( eukaryotes ):
>     http://www.cbcb.umd.edu/software/GlimmerHMM/
> GlimmerM ( eukaryotes ):
>     http://www.cbcb.umd.edu/software/glimmerm/index.shtml
>     http://www.tigr.org/software/glimmerm/
> 
>     I suspect Bio::Tools::Glimmer only parses GlimmerM, *maybe*
> GlimmerHMM, but not Glimmer 2.X or Glimmer 3.X.

I also noticed this last year some time but never got around to deducing 
the various flavours, and forgot about it... :-)

I work with Bacteria and have only used "Glimmer 2.x" and "Glimmer 3.x".

I will try and produce output files for all four variants today, then we 
can nut out a improvement path for Bio::Tools::Glimmer.

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia



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