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. 1997 Mar 1;25(5):955-64.
doi: 10.1093/nar/25.5.955.

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

T M Lowe  1 , S R Eddy
Affiliations

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

T M Lowe et al. Nucleic Acids Res. .

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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