Nucleic Acids Research, Vol 25, Issue 5 955-964, Copyright © 1997 by Oxford University Press
TM Lowe and SR Eddy
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.
ARTICLES
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.
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