tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TLDR
A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.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.read more
Citations
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Journal ArticleDOI
Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains
Laurence Rohmer,Christine Fong,Simone Abmayr,Michael Wasnick,Theodore J. Larson Freeman,Matthew C. Radey,Tina Guina,Kerstin Svensson,Kerstin Svensson,Hillary S. Hayden,Michael A. Jacobs,Larry A. Gallagher,Colin Manoil,Robert K. Ernst,Becky Drees,Danielle Buckley,Eric Haugen,Donald Bovee,Yang Zhou,Jean Chang,Ruth Levy,Regina Lim,Will Gillett,Don Guenthener,Allison Kang,Scott A. Shaffer,Greg K. Taylor,Jinzhi Chen,Byron Gallis,David A. D'Argenio,Mats Forsman,Maynard V. Olson,David R. Goodlett,Rajinder Kaul,Samuel I. Miller,Mitchell J. Brittnacher +35 more
TL;DR: The chronology of events suggests a substantial role for genetic drift in the formation of pseudogenes in Francisella genomes, which may be shared by pathogens from other species.
Journal ArticleDOI
Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation
Cristina Pop,Silvi Rouskin,Nicholas T. Ingolia,Lu Han,Eric M. Phizicky,Jonathan S. Weissman,Daphne Koller +6 more
TL;DR: It is shown that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA, and correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes.
Journal ArticleDOI
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.
Hiroyuki Ogata,Patricia Renesto,Stéphane Audic,Catherine Robert,Guillaume Blanc,Pierre-Edouard Fournier,Hugues Parinello,Jean-Michel Claverie,Didier Raoult +8 more
TL;DR: The sequenced genome of Rickettsia felis demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria.
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The Complete Genome and Proteome of Mycoplasma mobile
Jacob D. Jaffe,Nicole Stange-Thomann,Cherylyn Smith,David DeCaprio,Sheila Fisher,Jonathan Butler,Sarah E. Calvo,Tim Elkins,Michael Fitzgerald,Nabil Hafez,Chinnappa D. Kodira,John E. Major,Shunguang Wang,Jane E. Wilkinson,Robert Nicol,Chad Nusbaum,Bruce W. Birren,Howard C. Berg,George M. Church +18 more
TL;DR: For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins, including a long repeating unit of DNA of approximately 2435 bp present in five complete copies.
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Computational Genomics of Noncoding RNA Genes
TL;DR: The number of known noncoding RNA genes is expanding rapidly and computational genomics faces a new set of challenges to address these challenges.
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