tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
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 approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
Lowe
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Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
Eddy
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D000818:Animals; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D016678:Genome; D007438:Introns; D012313:RNA / Q000235:genetics; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D000077278:RNA, Mitochondrial; D012343:RNA, Transfer / Q000032:analysis / Q000235:genetics*; D012345:RNA, Transfer, Amino Acid-Specific / Q000235:genetics; D012984:Software
D012329:RNA, Bacterial; D000077278:RNA, Mitochondrial; D012345:RNA, Transfer, Amino Acid-Specific; C036928:tRNA, selenocysteine-; D012313:RNA; D012343:RNA, Transfer