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
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The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.
Eva Trost,Lisa Ott,Jessica Schneider,Jasmin Schröder,Sebastian Jaenicke,Alexander Goesmann,Peter Husemann,Jens Stoye,Fernanda Alves Dorella,Flávia S. Rocha,Siomar de Castro Soares,Vivian D'Afonseca,Anderson Miyoshi,Jerónimo Saiz Ruiz,Artur Silva,Vasco Azevedo,Andreas Burkovski,Nicole Guiso,Olivier Join-Lambert,Samer Kayal,Andreas Tauch +20 more
TL;DR: The functional data deduced from the genome sequencing and the extended knowledge of virulence factors indicate that the human isolate C. pseudotuberculosis FRC41 is equipped with a distinct gene set promoting its survival under unfavorable environmental conditions encountered in the mammalian host.
Journal ArticleDOI
Klebsiella Phage ΦK64-1 Encodes Multiple Depolymerases for Multiple Host Capsular Types.
Yi Jiun Pan,Tzu Lung Lin,Ching Ching Chen,Yun Ting Tsai,Yi Hsiang Cheng,Yi Yin Chen,Pei-Fang Hsieh,Yi Tsung Lin,Jin-Town Wang +8 more
TL;DR: Nine functional capsule depolymerase-encoding genes in a bacteriophage are identified and correlated activities of the gene products to all ten hosts of this phage, providing an example of carriage of multiple depolymersases in a phage with a wide capsular type host spectrum.
Journal ArticleDOI
Complete genome sequence of the Medicago microsymbiont Ensifer ( Sinorhizobium ) medicae strain WSM419
Wayne Reeve,Patrick S. G. Chain,Patrick S. G. Chain,Graham O’Hara,Julie Ardley,Kemanthi Nandesena,Lambert Bräu,Ravi Tiwari,Stephanie Malfatti,Stephanie Malfatti,Hajnalka Kiss,Hajnalka Kiss,Alla Lapidus,Alex Copeland,Matt Nolan,Miriam Land,Miriam Land,Loren Hauser,Loren Hauser,Yun Juan Chang,Yun Juan Chang,Natalia Ivanova,Konstantinos Mavromatis,Victor Markowitz,Nikos C. Kyrpides,Margaret Gollagher,Ron Yates,Michael J. Dilworth,John Howieson +28 more
TL;DR: This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils and it is revealed that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes.
Journal ArticleDOI
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Nyok-Sean Lau,Yuko Makita,Mika Kawashima,Todd D. Taylor,Shinji Kondo,Ahmad Sofiman Othman,Alexander Chong Shu-Chien,Minami Matsui +7 more
TL;DR: The data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex.
Journal ArticleDOI
Characterization of two polyvalent phages infecting Enterobacteriaceae.
Sana Hamdi,Geneviève M. Rousseau,Simon J. Labrie,Denise M. Tremblay,Rim Saïed Kourda,Karim Ben Slama,Sylvain Moineau +6 more
TL;DR: Two novel virulent phages are isolated and characterized using a strain of Shigella flexneri as host bacterium and it is suggested that they may be useful for controlling bacterial populations.
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