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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Proceedings ArticleDOI
Local similarity in RNA secondary structures
TL;DR: A systematic treatment of alignment distance and local similarity algorithms on trees and forests, and how potential regulatory motifs can be discovered solely by their structural preservation, and independent of their sequence conservation and position.
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Calculating nucleic acid secondary structure.
TL;DR: A complete set of DNA energy parameters is now available and the RNA parameters have been improved and a number of new computer algorithms combine covariation analysis with energy methods.
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The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.
Lisa Klasson,Joakim Westberg,Panagiotis Sapountzis,Kristina Näslund,Ylva Lutnaes,Alistair C. Darby,Zoe Veneti,Lanming Chen,Henk R. Braig,Roger A. Garrett,Kostas Bourtzis,Siv G. E. Andersson +11 more
TL;DR: The results suggest that the transmission dynamics of Wolbachia and the opportunity for coinfections have created a freely recombining intracellular bacterial community with mosaic genomes.
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Exploring the Mycobacteriophage Metaproteome: Phage Genomics as an Educational Platform
Graham F. Hatfull,Marisa L. Pedulla,Deborah Jacobs-Sera,Pauline M Cichon,Amy Foley,Michael E. Ford,Rebecca M Gonda,Jennifer M. Houtz,Andrew J. Hryckowian,Vanessa A Kelchner,Swathi Namburi,Kostandin V Pajcini,Mark G Popovich,Donald T Schleicher,Brian Simanek,Alexis L. Smith,G. Zdanowicz,Vanaja Kumar,Craig L. Peebles,William R. Jacobs,Jeffrey G. Lawrence,Roger W. Hendrix +21 more
TL;DR: The abundance and diversity of phages, the simplicity ofphage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.
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The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.
Eugeni Belda,Eugeni Belda,Ruben G. A. van Heck,Maria Jose Lopez-Sanchez,Stéphane Cruveiller,Valérie Barbe,Claire M. Fraser,Hans-Peter Klenk,Jörn Petersen,Anne Morgat,Pablo I. Nikel,David Vallenet,Zoé Rouy,Agnieszka Sekowska,Vitor A. P. Martins dos Santos,Víctor de Lorenzo,Antoine Danchin,Claudine Médigue +17 more
TL;DR: The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology.
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