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 genome sequence of the model ascomycete fungus Podospora anserina
Eric Espagne,Olivier Lespinet,Fabienne Malagnac,Fabienne Malagnac,Corinne Da Silva,Olivier Jaillon,Betina M. Porcel,Arnaud Couloux,Jean-Marc Aury,Béatrice Segurens,Julie Poulain,Véronique Anthouard,Sandrine Grossetete,Hamid Khalili,Evelyne Coppin,Michelle Dequard-Chablat,Marguerite Picard,Véronique Contamine,Sylvie Arnaise,Anne Bourdais,Véronique Berteaux-Lecellier,Daniel Gautheret,Ronald P. de Vries,Evy Battaglia,Pedro M. Coutinho,Etienne Danchin,Bernard Henrissat,Riyad El Khoury,Annie Sainsard-Chanet,Annie Sainsard-Chanet,Antoine Boivin,Antoine Boivin,Bérangère Pinan-Lucarré,Carole H. Sellem,Robert Debuchy,Patrick Wincker,Jean Weissenbach,Philippe Silar,Philippe Silar +38 more
TL;DR: The features of the P.Anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
Journal ArticleDOI
RSEARCH: finding homologs of single structured RNA sequences.
Robert J. Klein,Sean R. Eddy +1 more
TL;DR: A program that takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs, called RSEARCH, which outperforms primary sequence programs in finding homologs of structured RNA sequences.
Journal ArticleDOI
Query-dependent banding (QDB) for faster RNA similarity searches.
Eric P. Nawrocki,Sean R. Eddy +1 more
TL;DR: In this article, an acceleration method called query-dependent banding (QDB) is proposed, which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database.
Journal ArticleDOI
The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)
Meng Yang,Meng Yang,Xiaowei Zhang,Xiaowei Zhang,Guiming Liu,Guiming Liu,Yuxin Yin,Yuxin Yin,Kaifu Chen,Kaifu Chen,Quanzheng Yun,Quanzheng Yun,Duojun Zhao,Duojun Zhao,Ibrahim S. Al-Mssallem,Ibrahim S. Al-Mssallem,Jun Yu,Jun Yu +17 more
TL;DR: Unlike most monocots, date palm has a typical cp genome similar to that of tobacco—with little rearrangement and gene loss or gain.
Journal ArticleDOI
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
Marcel Huntemann,Natalia Ivanova,Konstantinos Mavromatis,Konstantinos Mavromatis,H. James Tripp,David Paez-Espino,Krishnaveni Palaniappan,Ernest Szeto,Manoj Pillay,I-Min A. Chen,Amrita Pati,Torben Nielsen,Victor Markowitz,Nikos C. Kyrpides +13 more
TL;DR: The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Micro microbial Genome comparative analysis system.
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