[Blends-commit] r3125 - /projects/debug/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Thu Jan 26 22:14:54 2012
New Revision: 3125

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3125
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=3125&op=diff
==============================================================================
--- projects/debug/tasks/bio (original)
+++ projects/debug/tasks/bio Thu Jan 26 22:14:54 2012
@@ -22,40 +22,3 @@
  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.
-
-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
-Comment: There is a Gentoo page featuring some projects we do not have mentioned here:
-         http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en
-Comment: Phylogenie centric Ubuntu derivative with some additional derivatives
-	 http://www.eve.ucdavis.edu/rcthomson/phylis/
-Comment: SEQanswers: The next generation sequencing community
-	 http://seqanswers.com/forums/showthread.php?t=43
-Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)