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

Mark Johnson johnsonm at gmail.com
Tue Sep 19 11:33:22 EDT 2006


    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.
    People do seem to be confused, see Michael Watson's post to
bioperl-l on 10/18/2004:
http://bioperl.org/pipermail/bioperl-l/2004-October/017112.html.
    It seems that Glimmer is really more of a 'family' of programs.
Should there be one module that tries to parse all the different
output formats, or should there be Bio::Tools::Glimmer2,
Bio::Tools::Glimmer3, Bio::Tools::GlimmerHMM, Bio::Tools::GlimmerM?
I'm presently leaning towards the latter, and would not be opposed to
working on Glimmer2 and Glimmer3 myself, as I'm going to need them.
    Comments, suggestions, opposition, rotten fruit?


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