tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Open Access
- 1 March 1997
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 25 (5) , 0955-964
- https://doi.org/10.1093/nar/25.5.0955
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 ∼30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudo-genes.Keywords
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