[Blends-commit] r3120 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Tue Jan 24 16:17:46 2012
New Revision: 3120

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3120
Log:
Added hhsuite

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=3120&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Tue Jan 24 16:17:46 2012
@@ -3909,6 +3909,32 @@
  alternative sequencing methods for a sequence-based project, e.g. should the
  library be paired-end or not, how many reads should be sequenced.
 
+Depends: hhsuite
+Homepage: http://toolkit.genzentrum.lmu.de/sections/search
+License: GPL-3.0+
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
+WNPP: 656626
+Responsible: Laszlo Kajan <lkajan at rostlab.org>
+Pkg-Description: sensitive protein sequence searching based on HMM-HMM alignment
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ It contains HHsearch and HHblits among other programs and utilities.
+ .
+ HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
+ and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
+ proteins. HHsearch is often used for protein structure prediction to detect
+ homologous templates and to build highly accurate query-template pairwise
+ alignments for homology modeling.
+ .
+ HHblits can build high-quality MSAs starting from single sequences or from
+ MSAs. It transforms these into a query HMM and, using an iterative search
+ strategy, adds significantly similar sequences from the previous search to
+ the updated query HMM for the next search iteration. Compared to PSI-BLAST,
+ HHblits is faster, up to twice as sensitive and produces more accurate
+ alignments.
+
+
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html