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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Journal ArticleDOI
Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.
TL;DR: REPCLASS is introduced, a tool that automates the classification of TE sequences and shows that the program can classify accurately virtually any known TE types, and is validated as a powerful tool to explore the repetitive DNA landscapes of eukaryotes.
Journal ArticleDOI
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.
Sara E. Blumer-Schuette,Sara E. Blumer-Schuette,Richard J. Giannone,Jeffrey V. Zurawski,Jeffrey V. Zurawski,Inci Ozdemir,Inci Ozdemir,Qin Ma,Qin Ma,Yanbin Yin,Yanbin Yin,Ying Xu,Ying Xu,Irena Kataeva,Irena Kataeva,Farris L. Poole,Farris L. Poole,Michael W. W. Adams,Michael W. W. Adams,Scott D. Hamilton-Brehm,James Elkins,Frank W. Larimer,Miriam Land,Loren Hauser,Robert W. Cottingham,Robert L. Hettich,Robert M. Kelly,Robert M. Kelly +27 more
TL;DR: Taking into account the core genomes, pangenomes, and individual genomes, the ancestral Caldicellulosiruptor was likely cellulolytic and evolved, in some cases, into species that lost the ability to degrade crystalline cellulose while maintaining the capacity to hydrolyze amorphous cellulose and hemICEllulose.
Journal ArticleDOI
Current View on Phytoplasma Genomes and Encoded Metabolism
TL;DR: Comparison analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP, and general differences are obvious between different phylogenetic subgroups.
Journal ArticleDOI
Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced.
TL;DR: A novel giant retroelement, named Ogre, which is over 22 kb long and makes up at least 5% of the pea (Pisum sativum L.) genome and is possible to speculate about its recent amplification in the genomes of pea and other legume plants.
Journal ArticleDOI
Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.
Yasuo Yasui,Hideki Hirakawa,Mariko Ueno,Katsuhiro Matsui,Tomoyuki Katsube-Tanaka,Soo Jung Yang,Jotaro Aii,Shingo Sato,Masashi Mori +8 more
TL;DR: The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits and are used as a reference sequence for NGS-based markers.
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