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 resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration
Lihong Xiao,Ge Yang,Liechi Zhang,Xinhua Yang,Shuang Zhao,Zhongzhong Ji,Qing Zhou,Min Hu,Yu Wang,Ming Chen,Yu Xu,Haijing Jin,Xuan Xiao,Guipeng Hu,Fang Bao,Yong Hu,Ping Wan,Legong Li,Xin Deng,Tingyun Kuang,Cheng-Bin Xiang,Jian-Kang Zhu,Jian-Kang Zhu,Melvin J. Oliver,Yikun He +24 more
TL;DR: This is the first genome sequence of a Desiccation-tolerant extremophile, offering insight into the evolution of this important trait and a first look into the genome organization of desiccation tolerance.
Journal ArticleDOI
Dramatic Mitochondrial Gene Rearrangements in the Hermit Crab Pagurus longicarpus (Crustacea, Anomura)
TL;DR: The entire mitochondrial gene order of the crustacean Pagurus longicarpus was determined by sequencing all but approximately 300 bp of the mitochondrial genome, and the first major gene rearrangements found in the clade including Crustacea and Insecta are reported.
Journal ArticleDOI
Parallel Evolution of Truncated Transfer RNA Genes in Arachnid Mitochondrial Genomes
TL;DR: In this article, the authors provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders, and show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from many of the 22 tRNAs in the genomes of 4 out of 7 orders of spiders.
Journal ArticleDOI
Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence.
Joseph F. Petrosino,Qin Xiang,Sandor E. Karpathy,Huaiyang Jiang,Shailaja Yerrapragada,Yamei Liu,Jason Gioia,Lisa Hemphill,Arely Gonzalez,T. M. Raghavan,Akif Uzman,George E. Fox,Sarah K. Highlander,Mason V. Reichard,Rebecca J. Morton,Kenneth D. Clinkenbeard,George M. Weinstock +16 more
TL;DR: The complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978 is reported.
Journal ArticleDOI
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii.
TL;DR: It is proposed that this strain of C. ruddii can be viewed as a further step towards the degeneration of the former primary endosymbiont and its transformation in a subcellular new entity between living cells and organelles.
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