[Cdd-commits] r691 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Wed Apr  9 14:33:19 2008
New Revision: 691

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added GlimmerHMM


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Wed Apr  9 14:33:19 2008
@@ -970,3 +970,17 @@
  by default) on either side of that region. When a predicted gene
  overlaps an alignment we use the gene prediction to extend the
  boundaries of the output region.
+
+Depends: glimmerhmm
+Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
+License: DFSG free
+Pkg-Description: Eukaryotic Gene-Finding System
+ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
+ Model (GHMM). Although the gene finder conforms to the overall
+ mathematical framework of a GHMM, additionally it incorporates splice
+ site models adapted from the GeneSplicer program and a decision tree
+ adapted from GlimmerM. It also utilizes Interpolated Markov Models
+ for the coding and noncoding models . Currently, GlimmerHMM's GHMM
+ structure includes introns of each phase, intergenic regions, and
+ four types of exons (initial, internal, final, and single). A basic
+ user manual can be consulted here.