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
Homologues of nitrite reductases in ammonia‐oxidizing archaea: diversity and genomic context
Rita Bartossek,Rita Bartossek,Graeme W. Nicol,Anders Lanzén,Hans-Peter Klenk,Christa Schleper,Christa Schleper +6 more
TL;DR: The occurrence of genes encoding potential homologues of copper-dependent nitrite reductases (NirK) in ammonia-oxidizing archaea of soils and other environments using metagenomic approaches and PCR amplification is reported on.
Journal ArticleDOI
A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes)
TL;DR: This work confirms that vertebrates were the first host for stem group neodermatans and that the addition of a second, invertebrate, host was a single event occurring in the Trematoda+Cestoda lineage, and supports the hypothesis that the most recent common ancestor of the Neodermata giving rise to the Monogenea adopted vertebrate ectoparasitism as its initial life cycle pattern.
Journal ArticleDOI
The chromosomal organization of horizontal gene transfer in bacteria.
Pedro H. Oliveira,Pedro H. Oliveira,Marie Touchon,Marie Touchon,Jean Cury,Jean Cury,Eduardo P. C. Rocha,Eduardo P. C. Rocha +7 more
TL;DR: Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.
Journal ArticleDOI
Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): vicariance and recent demographic expansion in southern Atlantic forest
TL;DR: The data did not support the primary influence of geographical barriers or rivers in the intraspecific diversification of X. fuscus in the southern Atlantic forest, but supported the influence of isolation by geographical distance, recent vicariance events, and demographic expansions apparently related to Pleistocene and Holocene forest dynamics.
Journal ArticleDOI
Genome sequence of the plant pathogenic bacterium Dickeya dadantii 3937
Jeremy D. Glasner,Ching Hong Yang,Sylvie Reverchon,Nicole Hugouvieux-Cotte-Pattat,Guy Condemine,Jean Pierre Bohin,Frédérique Van Gijsegem,Shihui Yang,Thierry Franza,Dominique Expert,Guy Plunkett,Michael San Francisco,Amy O. Charkowski,Béatrice Py,Kenneth S. Bell,Lise Rauscher,Pablo Rodríguez-Palenzuela,Ariane Toussaint,Maria C. Holeva,Sheng Yang He,Vanessa Douet,Martine Boccara,Carlos Blanco,Ian K. Toth,Bradley D. Anderson,Bryan S. Biehl,Bryan S. Biehl,Bob Mau,Sarah M. Flynn,Frédéric Barras,Magdalen Lindeberg,Paul R. J. Birch,Shinji Tsuyumu,Xiangyang Shi,Michael E. Hibbing,Mee-Ngan Frances Yap,Mathilde Carpentier,Elie Dassa,Masahiro Umehara,Jihyun F. Kim,Michael Rusch,Pritin Soni,George F. Mayhew,Derrick E. Fouts,Steven R. Gill,Frederick R. Blattner,Noel T. Keen,Nicole T. Perna +47 more
TL;DR: The sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria, is presented.
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