[Debian-med-packaging] Bug#803542: ITP: trnascan-se -- detection of transfer RNA genes in genomic sequence

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>

* Package name    : trnascan-se
  Version         : 1.3.1
  Upstream Author : Todd Lowe <lowe at soe.ucsc.edu> and colleagues
* URL             : http://lowelab.ucsc.edu/tRNAscan-SE
* License         : GPL
  Programming Lang: C, Perl
  Description     : 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.

This package is useful for genome annotations and will be managed by the
Debian Med team.