[Blends-commit] r3126 - /projects/debug/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Thu Jan 26 22:18:14 2012
New Revision: 3126

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3126
Log:
Next try

Modified:
    projects/debug/tasks/bio

Modified: projects/debug/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/debug/tasks/bio?rev=3126&op=diff
==============================================================================
--- projects/debug/tasks/bio (original)
+++ projects/debug/tasks/bio Thu Jan 26 22:18:14 2012
@@ -3,22 +3,28 @@
  This metapackage will install Debian packages related to molecular biology,
  structural biology and bioinformatics for use in life sciences.
 
-Depends: grinder
-Responsible: Florent Angly <florent.angly at gmail.com>
-Homepage: http://sourceforge.net/projects/biogrinder/
-Vcs-Git: git://git.debian.org/debian-med/grinder.git
-Vcs-Browser: http://git.debian.org/?p=debian-med/grinder.git
-License: GPL-3+
-Pkg-Description: Versatile omics shotgun and amplicon sequencing read simulator
- Grinder is a versatile program to create random shotgun and amplicon sequence
- libraries based on DNA, RNA or proteic reference sequences provided in a
- FASTA file.
+
+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.
  .
- Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,
- proteomic, metaproteomic shotgun and amplicon datasets from current
- sequencing technologies such as Sanger, 454, Illumina. These simulated
- datasets can be used to test the accuracy of bioinformatic tools under
- specific hypothesis, e.g. with or without sequencing errors, or with low or
- high community diversity. Grinder may also be used to help decide between
- alternative sequencing methods for a sequence-based project, e.g. should the
- library be paired-end or not, how many reads should be sequenced.
+ 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.