[Blends-commit] r2661 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Mon Feb  7 15:42:12 2011
New Revision: 2661

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2661
Log:
Added sap

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=2661&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Feb  7 15:42:12 2011
@@ -2693,6 +2693,7 @@
 Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
 License: GPL (except two algorithms)
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Enhances: t-coffee
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
 Pkg-Description: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
  PRANK is a probabilistic multiple alignment program for DNA, codon
@@ -2722,6 +2723,7 @@
  differences between PRANK and traditional progressive alignment
  methods.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+ Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee)
 
 Comment: priam
  BioLinux contains a priam package which is available at
@@ -3424,6 +3426,33 @@
 Remark: Precondition for T-Coffee
  see http://wiki.debian.org/DebianMed/TCoffee
 
+Depends: sap
+Homepage: http://mathbio.nimr.mrc.ac.uk/wiki/Software#SAP
+License: GPL v3
+Enhances: t-coffee
+Pkg-Description: Pairwise protein structure alignment via double dynamic programming
+ In contrast to DNA, proteins exhibit an apparently unlimited variety of
+ structure. This is a necessary requirement of the vast array of
+ differing functions that they perform in the maintainance of life,
+ again, in contrast to the relatively static archival function of DNA.
+ Not only do we observe a bewildering variety of form but even within a
+ common structure, there is variation in the lengths and orientation
+ substructures. Such variation is both a reflection on the very long time
+ periods over which some structures have diverged and also a consequence
+ of the fact that proteins cannot be completely rigid bodies but must
+ have flexibility to accommodate the structural changes that are almost
+ always necessary for them to perform their functions. These aspects make
+ comparing structure and finding structural similarity over long
+ divergence times very difficult. Indeed, computationally, the problem of
+ recognizing similarity is one of three-dimensional pattern recognition,
+ which is a notoriously difficult problem for computers to perform. In
+ this chapter, guidance is provided on the use of a flexible structure
+ comparison method that overcomes many of the problems of comparing
+ protein structures that may exhibit only weak similarity.
+Published-URL: http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-368-2:19
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html