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

by: TM Lowe, SR Eddy

Nucleic Acids Res, Vol. 25, No. 5. (1 March 1997), pp. 955-964.

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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.

@article{Lowe1997, 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.}, address = {Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA.}, author = {Lowe, T. M. and Eddy, S. R. }, citeulike-article-id = {94462}, doi = {http://dx.doi.org/10.1093/nar/25.5.955}, issn = {0305-1048}, journal = {Nucleic Acids Res}, keywords = {covariance, prediction, trna}, month = {March}, number = {5}, pages = {955--964}, posted-at = {2006-06-09 19:28:48}, priority = {0}, title = {tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.}, url = {http://dx.doi.org/10.1093/nar/25.5.955}, volume = {25}, year = {1997} }

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TY - JOUR ID - Lowe1997 L3 - citeulike-article-id:94462 TI - tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. JF - Nucleic Acids Res VL - 25 IS - 5 SP - 955 EP - 964 AD - Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA. SN - 0305-1048 N2 - 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. KW - covariance KW - prediction KW - trna AU - Lowe, TM AU - Eddy, SR PY - 1997/03/01/ UR - http://dx.doi.org/10.1093/nar/25.5.955 ER -

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