tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
- Todd M. Lowe
- Sean R. Eddy
CiteWeb id: 19970000036
CiteWeb score: 7634
We describe a program, tRNAscan-SE, which 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.Links to full text of the publication: