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Nucleic Acids Res. Mar 1, 1997; 25(5): 955–964.
PMCID: PMC146525
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
T M Lowe and S R Eddy
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
Abstract
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.
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