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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The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.
Zhiwen Wang,Neil Hobson,Leonardo Galindo,Shilin Zhu,Daihu Shi,Joshua McDill,Linfeng Yang,Simon Hawkins,Godfrey Neutelings,Raju Datla,Georgina M. Lambert,David W. Galbraith,Christopher J. Grassa,Armando Geraldes,Quentin C. B. Cronk,Christopher A. Cullis,Prasanta K. Dash,Polumetla Ananda Kumar,Sylvie Cloutier,Sylvie Cloutier,Andrew G. Sharpe,Gane Ka-Shu Wong,Jun Wang,Michael K. Deyholos +23 more
TL;DR: Results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
Journal ArticleDOI
Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica
Alga Zuccaro,Urs Lahrmann,Ulrich Güldener,Gregor Langen,Stefanie Pfiffi,Dagmar Biedenkopf,Philip C. Wong,Birgit Samans,Carolin Grimm,Magdalena Basiewicz,Claude Murat,Francis Martin,Karl-Heinz Kogel +12 more
TL;DR: The findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.
Journal ArticleDOI
The genome of the simian and human malaria parasite Plasmodium knowlesi
Arnab Pain,Ulrike Böhme,Andrew Berry,Karen Mungall,Robert D. Finn,Andrew P. Jackson,Tobias Mourier,Jaina Mistry,Erica M. Pasini,Martin Aslett,S. Balasubrammaniam,Karsten M. Borgwardt,Karen Brooks,Celine Carret,Tim Carver,Inna Cherevach,Tracey Chillingworth,Taane G. Clark,Taane G. Clark,Mary R. Galinski,Neil Hall,D. Harper,David Harris,Heidi Hauser,Al Ivens,Christoph S. Janssen,Thomas M. Keane,Natasha Larke,Stacey A. Lapp,Matthias Marti,Sharon Moule,Irmtraud M. Meyer,Douglas Ormond,Nicholas S. Peters,Mandy Sanders,S. Sanders,Tobias Sargeant,Tobias Sargeant,Mark Simmonds,Frances Smith,R. Squares,Scott Thurston,Adrian Tivey,Danielle Walker,Brian White,Eduard Zuiderwijk,Carol Churcher,Michael A. Quail,Alan F. Cowman,C. M. R. Turner,Marie-Adèle Rajandream,Clemens H. M. Kocken,Alan W. Thomas,Chris I. Newbold,Chris I. Newbold,Bart Barrell,Matthew Berriman +56 more
TL;DR: This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes.
Journal ArticleDOI
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.
Christian Marck,Henri Grosjean +1 more
TL;DR: It is found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist, and Archaea appears as an "intermediate domain" between Eukarya and Bacteria.
Journal ArticleDOI
A genomic catalog of Earth’s microbiomes
Stephen Nayfach,Simon Roux,Rekha Seshadri,Daniel W. Udwary,Neha Varghese,Frederik Schulz,Dongying Wu,David Paez-Espino,I-Min Chen,Marcel Huntemann,Krishna Palaniappan,Joshua Ladau,Supratim Mukherjee,T. B. K. Reddy,Torben Nielsen,Edward Kirton,José P. Faria,Janaka N. Edirisinghe,Christopher S. Henry,Sean P. Jungbluth,Dylan Chivian,Paramvir S. Dehal,Elisha M. Wood-Charlson,Adam P. Arkin,Susannah G. Tringe,Axel Visel,Tanja Woyke,Nigel J Mouncey,Natalia Ivanova,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +30 more
TL;DR: The utility of this collection of >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans is demonstrated for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses.
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