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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Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.
Michael P. McLeod,Michael P. McLeod,Xiang Qin,Sandor E. Karpathy,Sandor E. Karpathy,Jason Gioia,Sarah K. Highlander,George E. Fox,Thomas Z. McNeill,Thomas Z. McNeill,Huaiyang Jiang,Donna M. Muzny,Leni S. Jacob,Alicia Hawes,Erica Sodergren,Rachel Gill,Jennifer Hume,Maggie Morgan,Guangwei Fan,Anita G. Amin,Richard A. Gibbs,Chao Hong,Xue Jie Yu,David H. Walker,George M. Weinstock,George M. Weinstock,George M. Weinstock +26 more
TL;DR: The complete genome sequence of R. typhi is presented and a three-way comparison allowed further in silico analysis of the SpoT split genes, leading to propose that the stringent response system is still functional in these rickettsiae.
Journal ArticleDOI
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution
Guo-Qiang Zhang,Qing Xu,Chao Bian,Wen Chieh Tsai,Chuan Ming Yeh,Ke-Wei Liu,Kouki Yoshida,Liangsheng Zhang,Song Bin Chang,Fei Chen,Yu Shi,Yu Shi,Yong Yu Su,Yong Yu Su,Yong-Qiang Zhang,Li Jun Chen,Ya-Yi Yin,Min Lin,Huixia Huang,Hua Deng,Zhi Wen Wang,Shi Lin Zhu,Xiang Zhao,Cao Deng,Shan Ce Niu,Jie Huang,Meina Wang,Guo Hui Liu,Hai Jun Yang,Hai Jun Yang,Xin Ju Xiao,Yu Yun Hsiao,Wan Lin Wu,Wan Lin Wu,You Yi Chen,Nobutaka Mitsuda,Masaru Ohme-Takagi,Masaru Ohme-Takagi,Yi-Bo Luo,Yves Van de Peer,Zhong-Jian Liu,Zhong-Jian Liu,Zhong-Jian Liu +42 more
TL;DR: The first draft genome sequence of a lithophytic orchid, Dendrobium catenatum, is reported, predicting 28,910 protein-coding genes, and finding evidence of a whole genome duplication shared with Phalaenopsis.
Structural rna homology search and alignment using covariance models
Sean R. Eddy,Eric P. Nawrocki +1 more
TL;DR: Improvements are made to Covariance models by making them faster and more sensitive to remote homology, and introducing a query-dependent banding technique that makes scoring sequences more efficient by restricting the possible lengths of structural elements based on their probability given the model.
Journal ArticleDOI
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.
Garret Suen,Paul J. Weimer,David M. Stevenson,Frank O. Aylward,Frank O. Aylward,Julie Boyum,Jan Deneke,Colleen Drinkwater,Natalia Ivanova,Natalia Mikhailova,Olga Chertkov,Lynne Goodwin,Lynne Goodwin,Cameron R. Currie,Cameron R. Currie,David A. Mead,Phillip J. Brumm +16 more
TL;DR: The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.
Journal ArticleDOI
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
Shaobin Hou,Kira S. Makarova,Jimmy H. Saw,Jimmy H. Saw,Pavel Senin,Pavel Senin,Benjamin V. Ly,Zhemin Zhou,Yan Ren,Jianmei Wang,Michael Y. Galperin,Marina V. Omelchenko,Yuri I. Wolf,Natalya Yutin,Eugene V. Koonin,Matthew B. Stott,Bruce W. Mountain,Michelle A. Crowe,Angela V Smirnova,Peter F. Dunfield,Peter F. Dunfield,Lu Feng,Lei Wang,Maqsudul Alam +23 more
TL;DR: Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria, which supports the monophyly of the PVC superphylum.
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