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
Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks
TL;DR: The CRt genome is an extreme example of a symbiont genome caught in the act of genome reduction, and the comparison between CLEAA and CRt indicates that losses of particular genes early on in this process can potentially greatly influence the speed of this process.
Journal ArticleDOI
Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.
Jason W. Holder,Jil C. Ulrich,Anthony C. DeBono,Paul A. Godfrey,Christopher A. Desjardins,Jeremy Zucker,Jeremy Zucker,Qiandong Zeng,Alex L. B. Leach,Ion Ghiviriga,Christine Dancel,Thomas Abeel,Dirk Gevers,Chinnappa D. Kodira,Brian Desany,Jason P. Affourtit,Bruce W. Birren,Anthony J. Sinskey +17 more
TL;DR: In this paper, a comparative analysis of the 9.27 Mb R. opacus PD630 genome was performed and the results of the catabolic screen, phylogenetic analysis of TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.
Journal ArticleDOI
Structural Analysis of a Lotus japonicus Genome. V. Sequence Features and Mapping of Sixty-four TAC Clones Which Cover the 6.4 Mb Regions of the Genome
TL;DR: A total of 56 TAC clones with an average insert size of 100 kb were isolated from a TAC library of the Lotus japonicus genome based on the expressed sequences tags, cDNA and gene information, and their nucleotide sequences were determined according to the shot-gun based strategy.
Journal ArticleDOI
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy.
Yuan Yuan,Xiao-Hua Jin,Juan Liu,Xing Zhao,Jun-Hui Zhou,Xin Wang,De-Yi Wang,Chang-Jiang-Sheng Lai,Wei Xu,Jingwen Huang,Liangping Zha,Da-Hui Liu,Xiao Ma,Li Wang,Menyan Zhou,Zhi Jiang,Hu-Biao Meng,Hua-Sheng Peng,Yu-Ting Liang,Ruiqiang Li,Chao Jiang,Yu-Yang Zhao,Tie-Gui Nan,Yan Jin,Zhi-Lai Zhan,Jian Yang,Wenkai Jiang,Luqi Huang +27 more
TL;DR: The 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes is presented, which provides insights in adaptation to a lifestyle of heterotrophy.
Journal ArticleDOI
Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda).
TL;DR: The complete nucleotide sequence of the mitochondrial genome was determined for a harpacticoid copepod, Tigriopus japonicus (Crustacea), using an approach that employs a long polymerase chain reaction technique and primer walking, resulting in one of the smallest mitochondrial genomes in the arthropod lineage.
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