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
More filters
Journal ArticleDOI
Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential
Carl J. Yeoman,Suleyman Yildirim,Susan M. Thomas,A. Scott Durkin,Manolito Torralba,Granger G. Sutton,Christian J. Buhay,Yan Ding,Shannon Dugan-Rocha,Donna M. Muzny,Xiang Qin,Richard A. Gibbs,Steven R. Leigh,Rebecca M. Stumpf,Bryan A. White,Sarah K. Highlander,Karen E. Nelson,Brenda A. Wilson +17 more
TL;DR: Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.
Journal ArticleDOI
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics
Jukka Corander,Jukka Corander,Jukka Corander,Christophe Fraser,Michael U. Gutmann,Brian J. Arnold,William P. Hanage,Stephen D. Bentley,Marc Lipsitch,Nicholas J. Croucher +9 more
TL;DR: It is shown that pneumococcal lineages from multiple populations each have a distinct combination of intermediate-frequency genes, suggesting negative frequency-dependent selection drives post-vaccination population restructuring.
Journal ArticleDOI
The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae)
Fang Liao,Lin Wang,Song Wu,Yu-Ping Li,Lei Zhao,Guo-Ming Huang,Chun-Jing Niu,Yan-Qun Liu,Minggang Li +8 more
TL;DR: The phylogenetic analyses support the view that the H. cunea is closerly related to the Lymantria dispar than Ochrogaster lunifer, and support the hypothesis that Noctuoidea (H. cunesa, L. dispar, and O. lunifer) and Geometroida (Phthonandria atrilineata) are monophyletic.
Journal ArticleDOI
Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach
Meng Qi,Pan Wang,Pan Wang,Nicholas O'Toole,Perry S. Barboza,Emilio M. Ungerfeld,Mary Beth Leigh,L. Brent Selinger,Greg Butler,Adrian Tsang,Tim A. McAllister,Robert J. Forster +11 more
TL;DR: A snapshot of eukaryotic gene expression in the muskoxen rumen is provided, and a number of candidate genes coding for potentially valuable lignocellulolytic enzymes are identified.
Journal ArticleDOI
Sequence of the genome of Salmonella bacteriophage P22.
TL;DR: The sequence of the nonredundant region of the Salmonella enterica serovar Typhimurium temperate, serotype-converting bacteriophage P22 has been completed and many of the putative proteins show sequence relatedness to proteins from a great variety of other phages, supporting the hypothesis that this phage has evolved through the recombinational exchange of genetic information with other viruses.
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.
Related Papers (5)
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more