[Blends-commit] r3443 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Mon Jun 25 13:27:20 2012
New Revision: 3443

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3443
Log:
ssaha is now also in VCS (finally)

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=3443&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Jun 25 13:27:20 2012
@@ -425,6 +425,11 @@
  Version 1.6 is the last upstream version that works with GNUstep.  If
  newer versions are needed to work under Linux try to convince upstream to
  support GNUstep.
+
+Depends: ssaha
+Remark: Successor for ssaha2 available: smalt
+ The program smalt is from the same author is according to its author
+ faster and more precise than ssaha2 (except for sequences > 2000bp)
 
 Depends: strap
 License: GNU + some external components with different licenses
@@ -560,30 +565,6 @@
  and/or profiles from PROSITE against one or several protein sequences
  in Swiss-Prot or FASTA format. It requires two compiled external
  programs from the PFTOOLS, which are also distributed with the sources.
-
-Depends: ssaha
-Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
-License: GPL
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 425111
-Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
- SSAHA is a software tool for very fast matching and alignment of DNA
- sequences. It achieves its fast search speed by converting sequence
- information into a `hash table' data structure, which can then be
- searched very rapidly for matches. It was published by Ning Z,
- Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
- .
- SSAHA is the only free software of its category (fast search of nearly
- indentical sequences). The popular alternative, BLAT, is restricted to
- non-commercial use.
- .
- Unfortunately the source of its successor ssaha2
- http://www.sanger.ac.uk/Software/analysis/SSAHA2/
- can not be relieased as Open Source because it contains
- proprietary code.
-Remark: Successor for ssaha2 available: smalt
- The program smalt is from the same author is according to its author
- faster and more precise than ssaha2 (except for sequences > 2000bp)
 
 Depends: phylographer
 Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html