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
The genome of Rhizobium leguminosarum has recognizable core and accessory components
J. Peter W. Young,Lisa Crossman,Andrew W. B. Johnston,Nicholas R. Thomson,Zara Ghazoui,Katherine H Hull,Margaret Wexler,Andrew R. J. Curson,Jonathan D. Todd,Philip S. Poole,Tim H. Mauchline,Alison K. East,Michael A. Quail,Carol Churcher,Claire Arrowsmith,Inna Cherevach,Tracey Chillingworth,Kay Clarke,Ann Cronin,Paul Davis,Audrey Fraser,Zahra Hance,Heidi Hauser,Kay Jagels,Sharon Moule,Karen Mungall,Halina Norbertczak,Ester Rabbinowitsch,Mandy Sanders,Mark Simmonds,Sally Whitehead,Julian Parkhill +31 more
TL;DR: The genome of R. leguminosarum can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G-C, and located on the plasmids and chromosomal islands.
Journal ArticleDOI
Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing
Shuang-Xi Ren,Shuang-Xi Ren,Gang Fu,Xiu-Gao Jiang,Rong Zeng,You-Gang Miao,Hai Xu,Yi-Xuan Zhang,Hui Xiong,Gang Lu,Ling-Feng Lu,Hong-Quan Jiang,Jia Jia,Yuefeng Tu,Ju-Xing Jiang,Wenyi Gu,Yue-Qing Zhang,Yue-Qing Zhang,Zhen Cai,Haihui Sheng,Hai-Feng Yin,Yi Zhang,Genfeng Zhu,Ma Wan,Hong-Lei Huang,Zhen Qian,Shengyue Wang,Wei Ma,Zhijian Yao,Yan Shen,Boqin Qiang,Qi-Chang Xia,Xiaokui Guo,Antoine Danchin,Isabelle Saint Girons,Ronald L. Somerville,Yu-Mei Wen,Man-Hua Shi,Zhu Chen,Jianguo Xu,Guoping Zhao,Guoping Zhao +41 more
TL;DR: The complete genomic sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae is reported, consisting of a 4.33-megabase large chromosome and a 359-kilobase small chromosome, with a total of 4,768 predicted genes.
Journal ArticleDOI
Translation efficiency is determined by both codon bias and folding energy
TL;DR: It is testified that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels.
Journal ArticleDOI
Identification and classification of conserved RNA secondary structures in the human genome
Jakob Skou Pedersen,Gill Bejerano,Adam Siepel,Kate R. Rosenbloom,Kerstin Lindblad-Toh,Eric S. Lander,Jim Kent,Webb Miller,David Haussler +8 more
TL;DR: A general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functionalRNAs encoded in the human genome is developed and used to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs.
Journal ArticleDOI
Tissue-specific differences in human transfer RNA expression.
TL;DR: The findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.
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