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
Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
Daniel B. Sloan,Andrew J. Alverson,John P. Chuckalovcak,Martin Wu,David E. McCauley,Jeffrey D. Palmer,Douglas R. Taylor +6 more
TL;DR: A pair of species within the genus Silene have evolved the largest known mitochondrial genomes, coinciding with extreme changes in mutation rate, recombination activity, and genome structure.
Journal ArticleDOI
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
Qi Jin,Zhenghong Yuan,Jianguo Xu,Yu Wang,Yan Shen,Weichuan Lu,Jinhua Wang,Hong Liu,Jian Yang,Fan Yang,Xiaobing Zhang,Jiyu Zhang,Guowei Yang,Hongtao Wu,Di Qu,Jie Dong,Lilian Sun,Ying Xue,Ailan Zhao,Yishan Gao,Junping Zhu,Biao Kan,Keyue Ding,Shuxia Chen,Hongsong Cheng,Zhijian Yao,Bingkun He,Runsheng Chen,Dalong Ma,Boqin Qiang,Yu-Mei Wen,Yunde Hou,Jun Yu +32 more
TL;DR: The S.flexneri chromosome has, astonishingly, 314 IS elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12 strain and enterohemorrhagic O157:H7 strain of Escherichia coli.
Journal ArticleDOI
Symbiosis insights through metagenomic analysis of a microbial consortium
Tanja Woyke,Hanno Teeling,Natalia Ivanova,Marcel Huntemann,Michael Richter,Frank Oliver Gloeckner,Frank Oliver Gloeckner,Dario Boffelli,Dario Boffelli,Iain Anderson,Kerrie Barry,Harris Shapiro,Ernest Szeto,Nikos C. Kyrpides,Marc Mussmann,Rudolf Amann,Claudia Bergin,Caroline Ruehland,Edward M. Rubin,Edward M. Rubin,Nicole Dubilier +20 more
TL;DR: A metagenomic approach is used to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia to propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.
Journal ArticleDOI
A Bioinformatician's Guide to Metagenomics
TL;DR: In this article, the authors describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step, and provide recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies.
Journal ArticleDOI
Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228).
Yue-Qing Zhang,Shuang-Xi Ren,Hua-Lin Li,Yong-Xiang Wang,Gang Fu,Jian Yang,Zhiqiang Qin,You-Gang Miao,Wen-Yi Wang,Runsheng Chen,Yan Shen,Zhu Chen,Zhenghong Yuan,Guoping Zhao,Di Qu,Di Qu,Antoine Danchin,Yu-Mei Wen +17 more
TL;DR: The complete genome of Staphylococcus epidermidis strain ATCC 12228, a non‐biofilm forming, non‐infection associated strain used for detection of residual antibiotics in food products, was sequenced and the ica operon coding for the enzymes synthesizing interbacterial cellular polysaccharide is missing.
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