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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.