[Blends-commit] r1860 - projects/med/trunk/debian-med/tasks

[Debian Pure Blends Subversion Commit]

Author: tille
Date: Mon Aug 31 08:10:42 2009
New Revision: 1860
URL: http://svn.debian.org/viewsvn/blends?rev=1860&view=rev

Log:
Add lagan


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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1860&view=diff&r1=1860&r2=1859&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Aug 31 08:10:42 2009
@@ -3024,3 +3024,24 @@
  is the GeneOntology.
 
 Suggests: pdb2pqr
+
+Depends: lagan
+Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
+License: GPL
+Pkg-Description: highly parametrizable pairwise global alignment program
+ Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of
+ the Needleman-Wunsch algorithm around these anchors.
+ .
+ Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment.
+ M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic
+ tree. Alignments are aligned to other alignments using the sum-of-pairs metric.
+Remark: May be packaged in local repository
+ A local package is mentioned at
+ https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Local%20Debian%20Repository
+ but the package does not seem to be available publicly.  It might be a good idea to ask
+ there before starting packaging.
+Published-Title: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
+Published-Authors: Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow, Serafim Batzoglou
+Published-In: Genome Research 13(4):721-31.
+Published-Year: 2003
+Published-URL: http://lagan.stanford.edu/lagan_web/mlagan_gr.pdf