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
Genome annotation: from sequence to biology
TL;DR: The aim of high-quality annotation is to identify the key features of the genome — in particular, the genes and their products.
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Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
Jan P. Meier-Kolthoff,Richard L. Hahnke,Jörn Petersen,Carmen Scheuner,Victoria Michael,Anne Fiebig,Christine Rohde,Manfred Rohde,Berthold Fartmann,Lynne Goodwin,Olga Chertkov,T. B. K. Reddy,Amrita Pati,Natalia Ivanova,Victor Markowitz,Nikos C. Kyrpides,Nikos C. Kyrpides,Tanja Woyke,Markus Göker,Hans-Peter Klenk +19 more
TL;DR: Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies withinE.
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The language of genes
TL;DR: Many techniques used in bioinformatics, even if developed independently, may be seen to be grounded in linguistics, and further interweaving of these fields will be instrumental in extending the understanding of the language of life.
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The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana
TL;DR: The results of the comparative analysis between the rapeseed and Arabidopsis mitochondrial genomes suggest that higher plant mitochondria are extremely conservative with respect to coding sequences and somewhat conservative withrespect to RNA editing, but that non-coding parts of plant mitochondrial DNA are extraordinarily dynamic with respectto structural changes, sequence acquisition and/or sequence loss.
Journal ArticleDOI
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Joshua C. Stein,Yeisoo Yu,Dario Copetti,Dario Copetti,Derrick J. Zwickl,Li Zhang,Chengjun Zhang,Kapeel Chougule,Kapeel Chougule,Dongying Gao,Aiko Iwata,Jose Luis Goicoechea,Sharon Wei,Jun Wang,Yi Liao,Muhua Wang,Muhua Wang,Julie Jacquemin,Julie Jacquemin,Claude Becker,Dave Kudrna,Jianwei Zhang,Carlos E.M. Londono,Xiang Song,Seunghee Lee,Paul L. Sanchez,Paul L. Sanchez,Andrea Zuccolo,Andrea Zuccolo,Jetty S.S. Ammiraju,Jetty S.S. Ammiraju,Jayson Talag,Ann Danowitz,Luis F. Rivera,Andrea R. Gschwend,Christos Noutsos,Cheng chieh Wu,Cheng chieh Wu,Shu-Min Kao,Shu-Min Kao,Jhih wun Zeng,Fu Jin Wei,Qiang Zhao,Qi Feng,Moaine El Baidouri,Marie-Christine Carpentier,Eric Lasserre,Richard Cooke,Daniel da Rosa Farias,Luciano Carlos da Maia,Railson Schreinert dos Santos,Kevin G. Nyberg,Kenneth L. McNally,Ramil Mauleon,Nickolai Alexandrov,Jeremy Schmutz,Dave Flowers,Chuanzhu Fan,Detlef Weigel,Kshirod K. Jena,Thomas Wicker,Mingsheng Chen,Bin Han,Robert J Henry,Yue-Ie C. Hsing,Nori Kurata,Antonio Costa de Oliveira,Olivier Panaud,Scott A. Jackson,Carlos A. Machado,Michael J. Sanderson,Manyuan Long,Doreen Ware,Doreen Ware,Rod A. Wing,Rod A. Wing +75 more
TL;DR: This study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species and announcing many new haplotypes of potential use for future crop protection.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
Journal ArticleDOI
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann Rd,Adams,Owen White,Rebecca A. Clayton,Ewen F. Kirkness,Anthony R. Kerlavage,Carol J. Bult,J F Tomb,Brian Dougherty,Merrick Jm +9 more
TL;DR: An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence of the genome from the bacterium Haemophilus influenzae Rd.
Journal ArticleDOI
The minimal gene complement of Mycoplasma genitalium
Claire M. Fraser,Jeannine D. Gocayne,Owen White,Mark Raymond Adams,Rebecca A. Clayton,Robert D. Fleischmann,Carol J. Bult,Anthony R. Kerlavage,Granger G. Sutton,Jenny M. Kelley,Janice L. Fritchman,Janice Weidman,Keith V. Small,Mina Sandusky,Joyce Fuhrmann,David Nguyen,Teresa Utterback,D. Saudek,Cheryl Phillips,Joseph M. Merrick,J F Tomb,Brian Dougherty,Kenneth F. Bott,Ping Chuan Hu,Thomas Lucier,Scott N. Peterson,Hamilton O. Smith,Clyde A. Hutchison,J. Craig Venter +28 more
TL;DR: Comparison of the Mycoplasma genitalium genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
PatentDOI
COMPLETE GENOME SEQUENCE OF THE METHANOGENIC ARCHAEON, $i(METHANOCOCCUS JANNASCHII)
TL;DR: In this article, the complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58 and 16-kilobase pair extrachromosomal elements are described.
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