[Blends-commit] r2665 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Feb 11 13:44:15 2011
New Revision: 2665

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2665
Log:
Added abacas

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2665&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Feb 11 13:44:15 2011
@@ -3469,6 +3469,26 @@
  ancestry.
 Published-URL: http://www.genetics.org/cgi/content/abstract/genetics.110.120121v1
 
+Depends: abacas
+Homepage: http://abacas.sourceforge.net/
+License: GPL
+Language: Perl
+Pkg-Description: Algorithm Based Automatic Contiguation of Assembled Sequences
+ ABACAS is intended to rapidly contiguate (align, order, orientate),
+ visualize and design primers to close gaps on shotgun assembled contigs
+ based on a reference sequence.
+ .
+ ABACAS uses MUMmer to find alignment positions and identify syntenies
+ of assembled contigs against the reference. The output is then processed
+ to generate a pseudomolecule taking overlapping contigs and gaps in to
+ account. ABACAS generates a comparision file that can be used to
+ visualize ordered and oriented contigs in ACT. Synteny is represented by
+ red bars where colour intensity decreases with lower values of percent
+ identity between comparable blocks. Information on contigs such as the
+ orientation, percent identity, coverage and overlap with other contigs
+ can also be visualized by loading the outputted feature file on ACT.
+
+
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html
 Comment: There is a Gentoo page featuring some projects we do not have mentioned here: