[Cdd-commits] r1067 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Sep  8 12:41:58 2008
New Revision: 1067

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Sep  8 12:41:58 2008
@@ -2254,3 +2254,38 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: estscan
+Homepage: http://estscan.sourceforge.net/
+License: free
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detect coding regions in DNA sequences, even if of low quality
+ ESTScan is a program that can detect coding regions in DNA sequences,
+ even if they are of low quality. It will also detect and correct
+ sequencing errors that lead to fr ameshifts.
+ .
+ ESTScan is not a gene prediction program, nor is it an open reading
+ frame detector. In fact, its strength lies in the fact that it does
+ not require an open reading frame to detect a coding region. As a
+ result, the program may miss a few translated amino acids at either
+ the N or the C terminus, but will detect coding regions with high
+ selectivity and sensitivity.
+ .
+ Similarly to GENSCAN, ESTScan uses a Markov model to represent the
+ bias in hexanucleotide usage found in coding regions relative to
+ non-coding regions. Additionally, ESTScan allows insertions and
+ deletions when these improve the coding region statistics. Further
+ details can be found at:
+ http://www.ch.embnet.org/software/ESTScan2_help.html
+ .
+ References:
+ Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing
+ errors by combining Hidden Markov models Bioinformatics 19,
+ ii103-ii112.
+ Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
+ detecting, evaluating, and reconstructing potential coding regions in
+ EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html