[Cdd-commits] r862 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Fri Jun 27 12:50:05 2008
New Revision: 862

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri Jun 27 12:50:05 2008
@@ -1566,3 +1566,16 @@
  using de Bruijn graphs.  D.R. Zerbino and E. Birney. Genome Research
  18:821-829.'
 
+Recommends: trnascan-se
+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.