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.
Keywords
Transfer RNABiologyGeneticsGeneRNAComputational biologySequence (biology)Context (archaeology)SelenocysteineCovarianceBiochemistryMathematics
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Publication Info
- Year
- 1997
- Type
- article
- Volume
- 25
- Issue
- 5
- Pages
- 955-964
- Citations
- 10850
- Access
- Closed
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Cite This
Todd M. Lowe,
Sean R. Eddy
(1997).
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.
Nucleic Acids Research
, 25
(5)
, 955-964.
https://doi.org/10.1093/nar/25.5.955
Identifiers
- DOI
- 10.1093/nar/25.5.955