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
The Apostasia genome and the evolution of orchids
Guo-Qiang Zhang,Ke-Wei Liu,Zhen Li,Rolf Lohaus,Yu Yun Hsiao,Shan Ce Niu,Shan Ce Niu,Jie Yu Wang,Jie Yu Wang,Yao-Cheng Lin,Yao-Cheng Lin,Qing Xu,Li Jun Chen,Kouki Yoshida,Sumire Fujiwara,Zhi Wen Wang,Yong-Qiang Zhang,Nobutaka Mitsuda,Meina Wang,Guo Hui Liu,Lorenzo Pecoraro,Hui Xia Huang,Xin Ju Xiao,Min Lin,Xin Yi Wu,Wan Lin Wu,Wan Lin Wu,You Yi Chen,Song Bin Chang,Shingo Sakamoto,Masaru Ohme-Takagi,Masaru Ohme-Takagi,Masafumi Yagi,Si Jin Zeng,Si Jin Zeng,Ching Yu Shen,Chuan Ming Yeh,Yi-Bo Luo,Wen Chieh Tsai,Yves Van de Peer,Zhong Jian Liu +40 more
TL;DR: New light is shed on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
Journal ArticleDOI
The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus
Sebastian Suerbaum,Christine Josenhans,Torsten Sterzenbach,Bernd Drescher,Petra Brandt,Monica Bell,Marcus Dröge,Berthold Fartmann,Hans-Peter Fischer,Zhongming Ge,Andrea Hörster,Rudi Holland,Kerstin Klein,Jochen König,Ludwig Macko,George L. Mendz,Gerald Nyakatura,David B. Schauer,Zeli Shen,Jacqueline Weber,Matthias Frosch,James G. Fox +21 more
TL;DR: The complete genome sequence of H. hepaticus ATCC51449 is reported, suggesting a role of HHGI1 in pathogenicity and several genomic islets whose G+C content differs from the rest of the genome.
Journal ArticleDOI
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
Neil F. W. Saunders,Torsten Thomas,Paul M. G. Curmi,John S. Mattick,Elizabeth Kuczek,Rob Slade,John Davis,Peter D. Franzmann,David Boone,Karl Rusterholtz,Robert A. Feldman,Chris Gates,Shellie R. Bench,Kevin R. Sowers,Kristen Kadner,Andrea Aerts,Paramvir S. Dehal,Chris Detter,Tijana Glavina,Susan Lucas,Paul G. Richardson,Frank W. Larimer,Loren Hauser,Miriam Land,Ricardo Cavicchioli +24 more
TL;DR: Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins from cold-adapted Archaea, and indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles
Journal ArticleDOI
Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila
Nicolas Vodovar,David Vallenet,Stéphane Cruveiller,Zoé Rouy,Valérie Barbe,Carlos Acosta,Laurence Cattolico,Claire Jubin,Aurélie Lajus,Béatrice Ségurens,Benoit Vacherie,Patrick Wincker,Jean Weissenbach,Bruno Lemaitre,Claudine Médigue,Frédéric Boccard +15 more
TL;DR: Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified and contributed to P. entomophila's entomopathogenic properties.
Journal ArticleDOI
Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43.
Ying-Tsong Chen,Hwan-You Chang,Yi-Chyi Lai,Chao Chi Pan,Shih-Feng Tsai,Shih-Feng Tsai,Hwei-Ling Peng +6 more
TL;DR: The entire DNA sequence of pLVPK, which is a 219-kb virulence plasmid harbored in a bacteremic isolate of Klebsiella pneumoniae, is determined and the presence of 13 insertion sequences located mostly at the boundaries of the aforementioned gene clusters suggests that pL VPK was derived from a sequential assembly of various horizontally acquired DNA fragments.
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COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
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