[Blends-commit] r2659 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Mon Feb  7 15:29:16 2011
New Revision: 2659

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2659
Log:
Added pcma

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=2659&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Feb  7 15:29:16 2011
@@ -3372,6 +3372,7 @@
 Depends: blast+
 Homepage: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 License: same as blast2
+Enhances: t-coffee
 Pkg-Description: new suite of BLAST tools
  BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++
  Toolkit. The BLAST+ applications have a number of performance and
@@ -3380,7 +3381,31 @@
  (PubMed link).
  .
  Please note that binaries and options were changed.
-Remark: Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee)
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+
+Depends: pcma
+Homepage: ftp://iole.swmed.edu/pub/PCMA/
+License: non-free for commercial
+Enhances: t-coffee
+Pkg-Description: fast and accurate multiple sequence alignment based on profile consistency
+ PCMA (profile consistency multiple sequence alignment) is a progressive
+ multiple sequence alignment program that combines two different
+ alignment strategies. Highly similar sequences are aligned in a fast way
+ as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
+ applied to align the relatively divergent groups based on
+ profile–profile comparison and consistency. The scoring function for
+ local alignments of pre-aligned groups is based on a novel
+ profile–profile comparison method that is a generalization of the
+ PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
+ and accuracy in a flexible way and is suitable for aligning large
+ numbers of sequences. 
+Published-URL: http://bioinformatics.oxfordjournals.org/content/19/3/427.short
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+ .
+ Check with authors about licensing, they adopted code from clustalw which is now
+ free.  Thus a change might be possible
 
 
 Comment: Several related R packages are listed at CRAN: