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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  2. Seligmann, Hervé: Putative anticodons in mitochondrial trna sidearm loops: pocketknife tRNAs? (2014)
  3. Clote, Peter; Kranakis, Evangelos; Krizanc, Danny: Asymptotic number of hairpins of saturated RNA secondary structures (2013)
  4. Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge: On the page number of RNA secondary structures with pseudoknots (2012)
  5. Michel, Christian J.: Circular code motifs in transfer and 16S ribosomal RNAs: a possible translation code in genes (2012)
  6. Seligmann, Hervé: Overlapping genetic codes for overlapping frameshifted genes in Testudines, and \textitLepidochelysolivacea as special case (2012)
  7. Herbig, Alexander; Nieselt, Kay: Nocornac: characterization of non-coding rnas in prokaryotes (2011) ioport
  8. Seligmann, Hervé: Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion (2011)
  9. Clote, Peter: Introduction to special issue on RNA (2008)
  10. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  11. Naitoh, Ken: Inevitability of ntp: Information - energy carriers (2008) ioport
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  13. Davydov, Eugene; Batzoglou, Serafim: A computational model for RNA multiple structural alignment (2006)
  14. Kunisawa, Takashi: Dichotomy of major bacterial phyla inferred from gene arrangement comparisons (2006)
  15. 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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