[Cdd-commits] r690 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Wed Apr  9 12:27:48 2008
New Revision: 690

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Twain and ROSE as prospective packages


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Wed Apr  9 12:27:48 2008
@@ -930,3 +930,43 @@
  It finds associations of single or pairs of DNA
  variations with a phenotype and can retrieve
  SNP annotation from an online source.
+
+Depends: twain
+Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
+License: Open Source
+Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
+ TWAIN is a new syntenic genefinder which employs a Generalized Pair
+ Hidden Markov Model (GPHMM) to predict genes in two closely related
+ eukaryotic genomes simultaneously.  It utilizes the MUMmer package to
+ perform approximate alignment before applying a GPHMM based on an
+ enhanced version of the TigrScan gene finder.  TWAIN was written by
+ Bill Majoros and Mihaela Pertea while at The Institute for Genomic
+ Research (TIGR).
+ .
+ TWAIN consists of two components: (1) ROSE, the Region Of Synteny
+ Extractor, which identifies contiguous regions likely to contain one
+ or more syntenic genes, and (2) OASIS, a generalized pair hidden
+ Markov model (GPHMM) for predicting genes in the regions identified
+ by ROSE.  The system utilizes approximate alignments constructed by
+ the PROmer and NUCmer programs in the MUMmer package to assess
+ approximate alignment scores efficiently.  More detailed information
+ on the architecture of this system will be made available soon.
+ Slides from a talk at Computational Genomics 2004 are now available.
+
+Depends: rose
+Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
+License: Open Source
+Pkg-Description: Region-Of-Synteny Extractor
+ ROSE is a program which identifies regions between two genomes which
+ are likely to contain orthologous genes. The two genomes are given as
+ two multi fasta files of DNA sequences. The PROmer program from the
+ MUMmer package needs to be run first between the two genomes, and the
+ resulting delta file is then input to ROSE. If a previous annotation
+ is available for one or both genomes, then the coordinates of the
+ annotated genes from a genome can be optionally given as input in a
+ gff file. The gene coordinates will be used to guide the length of
+ the regions produced by ROSE. By default, when finding a region of
+ consistent alignments, ROSE will add a user-defined margin (1000 bp
+ by default) on either side of that region. When a predicted gene
+ overlaps an alignment we use the gene prediction to extend the
+ boundaries of the output region.