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
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
Fay-Wei Li,Fay-Wei Li,Paul Brouwer,Lorenzo Carretero-Paulet,Shifeng Cheng,Jan de Vries,Pierre-Marc Delaux,Ariana N. Eily,Nils Koppers,Li-Yaung Kuo,Zheng Li,Mathew Simenc,Ian Small,Eric K. Wafula,Stephany Angarita,Michael S. Barker,Andrea Bräutigam,Claude W. dePamphilis,Sven B. Gould,Prashant S. Hosmani,Yao Moan Huang,Bruno Huettel,Yoichiro Kato,Xin Liu,Steven Maere,Rose McDowell,Lukas A. Mueller,Klaas G.J. Nierop,Stefan A. Rensing,Tanner A. Robison,Carl J. Rothfels,Erin M. Sigel,Yue Song,Prakash R. Timilsena,Yves Van de Peer,Yves Van de Peer,Hongli Wang,Per K.I. Wilhelmsson,Paul G. Wolf,Xun Xu,Joshua P. Der,Henriette Schluepmann,Gane Ka-Shu Wong,Kathleen M. Pryer +43 more
TL;DR: The genomes of two fern species, Azolla filiculoides and Salvinia cucullata, are reported and insights into fern-specific whole-genome duplications, f Fern-specific insect-resistant gene evolution and fern–cyanobacterial symbiosis are provided.
Journal ArticleDOI
Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
Hidehiro Toh,Brian L. Weiss,Sarah A.H. Perkin,Atsushi Yamashita,Kenshiro Oshima,Masahira Hattori,Serap Aksoy +6 more
TL;DR: Sodalis represents an evolutionary intermediate transitioning from a free-living to a mutualistic lifestyle, and its chromosome encodes a complete flagella structure, key components of which are expressed in immature host developmental stages.
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Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.
Xinpeng Qi,Man-Wah Li,Min Xie,Xin Liu,Meng Ni,Guihua Shao,Chi Song,Aldrin Kay-Yuen Yim,Ye Tao,Fuk-Ling Wong,Sachiko Isobe,Chi-Fai Wong,Kwong-Sen Wong,Chunyan Xu,Chunqing Li,Ying Wang,Rui Guan,Fengming Sun,Guangyi Fan,Zhixia Xiao,Feng Zhou,Tsui-Hung Phang,Xuan Liu,Suk-Wah Tong,Ting-Fung Chan,Siu-Ming Yiu,Satoshi Tabata,Jian Wang,Xun Xu,Hon-Ming Lam +29 more
TL;DR: A combination of de novo sequencing data from this work and previous germplasm re-sequencing data is used to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance, and rapid gain-of-function tests show the protective effects of Gm CHX1 towards salt stress.
Journal ArticleDOI
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid.
Melanie J. Barnett,Robert F. Fisher,Ted Jones,Caridad Komp,A P Abola,Frédérique Barloy-Hubler,Leah Bowser,Delphine Capela,Francis Galibert,Jérôme Gouzy,Mani Gurjal,A Hong,Lucas Huizar,Richard W. Hyman,Daniel Kahn,Michael L. Kahn,Sue Kalman,David H. Keating,Curtis J. Palm,Melicent C. Peck,Ray Surzycki,Derek H. Wells,Kuo-Chen Yeh,Ronald W. Davis,Nancy A. Federspiel,Sharon R. Long +25 more
TL;DR: The complete 1,354,226-nt sequence of pSymA, which contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
Journal ArticleDOI
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.
TL;DR: al. as discussed by the authors employ a comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model.
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