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tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

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Lowe, Todd M., Eddy, Sean R.·1997·Nucleic Acids Research

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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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“RNAmmer and tRNAscan-SE were utilized to identify rRNA and tRNA genes, respectively.(14,15) Gview was used to construct basic genomic features.”
Method
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Authors: Lowe, T. M., & Eddy, S. R.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 1997-03-01
Volume: 25
Issue: 5
Pages: 955-964
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/25.5.955
OpenAlex: W2149429041
Cited by: 10,905
References: 1
FWCI: 10.24
Type: journal article
Language: en
Open access: green

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tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

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