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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A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.
Tannistha Nandi,Catherine Ong,Arvind Pratap Singh,Justin A Boddey,Timothy P. Atkins,Mitali Sarkar-Tyson,Angela E. Essex-Lopresti,Hui Hoon Chua,Talima Pearson,Jason F. Kreisberg,Christina Nilsson,Pramila N. Ariyaratne,Catherine M. Ronning,Liliana Losada,Yijun Ruan,Wing-Kin Sung,Donald E. Woods,Richard W. Titball,Richard W. Titball,Ifor R. Beacham,Ian R. Peak,Paul Keim,William C. Nierman,Patrick Tan,Patrick Tan +24 more
TL;DR: Functional experiments revealed that certain positively selected genes might enhance mammalian virulence by interacting with host cellular pathways or utilizing host nutrients, and establish Bp as a model system for studying the genetics of accidental virulence.
Journal ArticleDOI
Orione, a web-based framework for NGS analysis in microbiology
Gianmauro Cuccuru,Massimiliano Orsini,Andrea Pinna,Andrea Sbardellati,Nicola Soranzo,Antonella Travaglione,Paolo Uva,Gianluigi Zanetti,Giorgio Fotia +8 more
TL;DR: Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.
Journal ArticleDOI
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea
Yvan Zivanovic,Jean Armengaud,Arnaud Lagorce,Christophe Leplat,Philippe P. Guerin,Murielle Dutertre,Véronique Anthouard,Patrick Forterre,Patrick Wincker,Fabrice Confalonieri +9 more
TL;DR: This work is the first archaeal proteome investigation done at the stage of primary genome annotation and indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.
Journal ArticleDOI
Mitochondrial genetic code in cestodes
TL;DR: It is proposed that the flatworm mitochondrial code should be modified for cestodes, particularly, in an initiating methionine codon (GUG) and a terminating codons (UAA) based on results.
Journal ArticleDOI
Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L
Dong Keun Yi,Ki Joong Kim +1 more
TL;DR: The genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes.
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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