[Cdd-commits] r1081 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Sep 11 08:25:07 2008
New Revision: 1081

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added last-align


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Sep 11 08:25:07 2008
@@ -1604,34 +1604,61 @@
 Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/
 License: GPL
 Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence
- tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
- giving less than one false positive per 15 gigabases. Two previously described
- tRNA detection programs are used as fast, first-pass prefilters to identify
- candidate tRNAs, which are then analyzed by a highly selective tRNA covariance
- model. This work represents a practical application of RNA covariance models,
- which are general, probabilistic secondary structure profiles based on stochastic
- context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional
- extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine
- tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
+ tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence
+ while giving less than one false positive per 15 gigabases. Two
+ previously described tRNA detection programs are used as fast,
+ first-pass prefilters to identify candidate tRNAs, which are then
+ analyzed by a highly selective tRNA covariance model. This work
+ represents a practical application of RNA covariance models, which
+ are general, probabilistic secondary structure profiles based on
+ stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000
+ bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA
+ homologues such as selenocysteine tRNAs, tRNA-derived repetitive
+ elements and tRNA pseudogenes.
 
 Depends: beast-mcmc
 Homepage: http://beast.bio.ed.ac.uk/
 License: LGPL
 Pkg-Description: Bayesian MCMC analysis of molecular sequences
- BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
- It is entirely orientated towards rooted, time-measured phylogenies inferred using
- strict or relaxed molecular clock models. It can be used as a method of
- reconstructing phylogenies but is also a framework for testing evolutionary
- hypotheses without conditioning on a single tree topology. BEAST uses MCMC to
- average over tree space, so that each tree is weighted proportional to its
- posterior probability. We include a simple to use user-interface program for
- setting up standard analyses and a suit of programs for analysing the results.
+ BEAST is a cross-platform program for Bayesian MCMC analysis of
+ molecular sequences.  It is entirely orientated towards rooted,
+ time-measured phylogenies inferred using strict or relaxed molecular
+ clock models. It can be used as a method of reconstructing
+ phylogenies but is also a framework for testing evolutionary
+ hypotheses without conditioning on a single tree topology. BEAST uses
+ MCMC to average over tree space, so that each tree is weighted
+ proportional to its posterior probability. We include a simple to use
+ user-interface program for setting up standard analyses and a suit of
+ programs for analysing the results.
  .
  The source is avialable at http://code.google.com/p/beast-mcmc/ .
  .
  Please note: There is a Debian package beast which is completely unrelated
  to this project.
 
+Depends: last-align
+Homepage://last.cbrc.jp/
+License: GPL-3+
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 498562
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/last-align/trunk/?rev=0&sc=0
+Pkg-Description: genome-scale comparison of biological sequences.
+ LAST is software for comparing and aligning sequences, typically DNA
+ or protein sequences. LAST is similar to BLAST, but it copes better
+ with very large amounts of sequence data. Here are two things LAST is
+ good at:
+ .
+  * Comparing large (e.g. mammalian) genomes.
+  * Mapping lots of sequence tags onto a genome.
+ .
+ The main technical innovation is that LAST finds initial matches
+ based on their multiplicity, instead of using a fixed size
+ (e.g. BLAST uses 11-mers).  This allows us to map tags to genomes
+ without repeat-masking, without becoming overwhelmed by repetitive
+ hits. To find these variable-sized matches, it uses a suffix array
+ (inspired by Vmatch). To achieve high sensitivity, it uses a
+ discontiguous suffix array, analogous to spaced seeds.
+
 Depends: artemis
 Homepage: http://www.sanger.ac.uk/Software/Artemis/
 License: GPL 2+