tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence - PubMed (original) (raw)
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
T M Lowe et al. Nucleic Acids Res. 1997.
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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References
- J Mol Biol. 1993 Mar 5;230(1):51-6 - PubMed
- Comput Appl Biosci. 1992 Feb;8(1):45-8 - PubMed
- J Bacteriol. 1993 Aug;175(16):5091-6 - PubMed
- Nat Genet. 1993 Aug;4(4):332-3 - PubMed
- Gene. 1993 Dec 15;135(1-2):57-66 - PubMed
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