Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
* Package name : trnascan-se Version : 1.3.1 Upstream Author : Todd Lowe <l...@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.
