[Cdd-commits] r692 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Wed Apr  9 14:38:41 2008
New Revision: 692

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


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 14:38:41 2008
@@ -973,7 +973,7 @@
 
 Depends: glimmerhmm
 Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
-License: DFSG free
+License: Artistic
 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
@@ -984,3 +984,29 @@
  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.
+
+Depends: genezilla
+Homepage: http://www.genezilla.org/
+License: Artistic
+Pkg-Description: eukaryotic gene finder
+ GeneZilla is a state-of-the-art program for computational prediction
+ of protein-coding genes in eukaryotic DNA, and is based on the
+ Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
+ and GENIE. It is highly reconfigurable and includes software for
+ retraining by the end-user. It is written in highly optimized C++ and
+ runs under most UNIX/Linux platforms. The run time and memory
+ requirements are linear in the sequence length, and are in general
+ much better than those of competing systems, due to GeneZilla's novel
+ decoding algorithm. Graph-theoretic representations of the high
+ scoring open reading frames are provided, allowing for exploration of
+ sub-optimal gene models. It utilizes Interpolated Markov Models
+ (IMMs), Maximal Dependence Decomposition (MDD), and includes states
+ for signal peptides, branch points, TATA boxes, CAP sites, and will
+ soon model CpG islands as well.
+ .
+ GeneZilla is an open-source project hosted at bioinformatics.org and
+ currently consists of ~20,000 lines of code.  GeneZilla evolved out
+ of the ab initio eukaryotic gene finder TIGRscan, which was developed
+ at The Institute for Genomic Research over a 3-year period under NIH
+ grants R01-LM06845 and R01-LM007938, and which served as the basis
+ for the comparative gene finder TWAIN.