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.

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  3. Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
  4. Michel, Christian J.: Circular code motifs in transfer and 16S ribosomal RNAs: a possible translation code in genes (2012)
  5. Seligmann, Hervé: Overlapping genetic codes for overlapping frameshifted genes in Testudines, and \itLepidochelys olivacea as special case (2012)
  6. Clote, Peter: Introduction to special issue on RNA (2008)
  7. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  8. Naitoh, Ken: Inevitability of ntp: Information - energy carriers (2008) ioport
  9. Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
  10. Davydov, Eugene; Batzoglou, Serafim: A computational model for RNA multiple structural alignment (2006)
  11. 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
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