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PMID: 9023104 Published · ppublish English Journal Article

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

Nucleic acids research ·Vol. 25 ·No. 5 ·1997-03-01 ·Pages 955-64

Lowe TM, Eddy SR

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.

MeSH Terms
Animals Databases, Factual Evaluation Studies as Topic Genome Introns RNA/genetics RNA, Bacterial/analysis,genetics RNA, Mitochondrial RNA, Transfer/analysis,genetics RNA, Transfer, Amino Acid-Specific/genetics Software
Chemicals
RNA, Bacterial RNA, Mitochondrial RNA, Transfer, Amino Acid-Specific tRNA, selenocysteine- RNA RNA, Transfer
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lowe T M
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
Eddy S R
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.5.955
Published
1997-03-01
Pages
955-64
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146525
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/25.5.955 PMC Full Text View journal details
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