[Cdd-commits] r694 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Wed Apr  9 20:50:15 2008
New Revision: 694

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


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 20:50:15 2008
@@ -1028,3 +1028,30 @@
  extensively tested on Drosophila melanogaster, but can be adapted to
  run on other species.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: jigsaw
+Homepage: http://www.cbcb.umd.edu/software/jigsaw/
+License: Artistic
+Pkg-Description: gene prediction using multiple sources of evidence
+ JIGSAW is a program designed to use the output from gene finders,
+ splice site prediction programs and sequence alignments to predict
+ gene models. The program provides an automated way to take advantage
+ of the many succsessful methods for computational gene prediction and
+ can provide substantial improvements in accuracy over an individual
+ gene prediction program.
+ .
+ JIGSAW is available for all species. It is tested on Human, Rice
+ (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
+ neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
+ fumigatus, Plasmodium falciparum and Plasmodium yoelii.
+ .
+ The linear combiner option is now available in the current JIGSAW
+ software distribution. This allows JIGSAW to be run without the use
+ of training data. A weight is assigned to each evidence source, and
+ gene predictions are based on a weighted voting scheme, yielding the
+ best 'consensus' predictions.
+ .
+ Predictions are now available for the ENCODE regions in Human and
+ viewable as custom tracks in the UCSC Human Genome
+ Browser. Predictions available for the Human genome and viewable as
+ custom tracks in the UCSC Human Genome Browser