[Cdd-commits] r749 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Wed May 21 14:06:09 2008
New Revision: 749

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Wed May 21 14:06:09 2008
@@ -1441,17 +1441,31 @@
 Depends: elph
 Homepage: http://www.cbcb.umd.edu/software/ELPH/
 License: Artistic
-Pkg-Description: Estimated Locations of (DNA) Pattern Hits
- ELPH is a general-purpose Gibbs sampler for finding motifs in a set
- of DNA or protein sequences. The program takes as input a set
- containing anywhere from a few dozen to thousands of sequences, and
- searches through them for the most common motif, assuming that each
- sequence contains one copy of the motif. We have used ELPH to find
- patterns such as ribosome binding sites (RBSs) and exon splicing
- enhancers (ESEs). See below for instructions on downloading the
- complete system, including source code.
+Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
+ ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs
+ sampler for finding motifs in a set of DNA or protein sequences. The
+ program takes as input a set containing anywhere from a few dozen to
+ thousands of sequences, and searches through them for the most common
+ motif, assuming that each sequence contains one copy of the motif. We
+ have used ELPH to find patterns such as ribosome binding sites (RBSs)
+ and exon splicing enhancers (ESEs). See below for instructions on
+ downloading the complete system, including source code.
  .
  An online tool that uses ELPH output for identifying exon splicing
  enhancers can be found at
  http://www.cbcb.umd.edu/software/SeeEse/index.html .
 Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: repeatfinder
+Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
+License: Artistic
+Pkg-Description: finding repetitive sequences complete and draft genomes
+ Two programs for finding repeats in genomic DNA sequences.  The first
+ program, described in the paper by Volfovsky et al. (2001) Genome
+ Biology is RepeatFinder.  A second program, designed specifically to
+ find repeats likely to confuse a genome assembly, is called
+ ClosureRepeatFinder.  The two programs are quite different and have
+ different purposes; RepeatFinder is intended to be the more
+ comprehensive approach.  Note that RepeatFinder depends on Stefan
+ Kurtz's REPuter.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)