tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. 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 ∼30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudo-genes.
Keywords for this software
References in zbMATH (referenced in 10 articles )
Showing results 1 to 10 of 10.
- Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
- Clote, Peter; Kranakis, Evangelos; Krizanc, Danny: Asymptotic number of hairpins of saturated RNA secondary structures (2013)
- Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
- Clote, Peter: Introduction to special issue on RNA (2008)
- Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
- Naitoh, Ken: Inevitability of ntp: Information - energy carriers (2008) ioport
- Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
- Davydov, Eugene; Batzoglou, Serafim: A computational model for RNA multiple structural alignment (2006)
- Song, Ying-Lei; Zhao, Ji-Zhen; Liu, Chun-Mei; Liu, Kan; Malmberg, Russell; Cai, Li-Ming: RNA structural homology search with a succinct stochastic grammar model (2005) ioport
- Durbin, Richard; Eddy, Sean R.; Krogh, Anders; Mitchison, Graeme: Biological sequence analysis. Probabilistic models of proteins and nucleic acids (1998)