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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Performance comparison of benchtop high-throughput sequencing platforms
Nicholas J. Loman,Raju Misra,Timothy J. Dallman,Chrystala Constantinidou,Saheer E. Gharbia,John Wain,John Wain,Mark J. Pallen +7 more
TL;DR: The performance of these instruments were compared by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011, and the MiSeq had the highest throughput per run and lowest error rates.
Journal ArticleDOI
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.
Dongwan D. Kang,Feng Li,Edward Kirton,Ashleigh Thomas,Rob Egan,Hong An,Zhong Wang,Zhong Wang,Zhong Wang +8 more
TL;DR: Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed, and recommends the community adopts Meta BAT 2 for their meetagenome binning experiments.
Journal ArticleDOI
Comparative genomics of the lactic acid bacteria
Kira S. Makarova,Alexei I. Slesarev,Yuri I. Wolf,Alexander V. Sorokin,Boris Mirkin,Eugene V. Koonin,Andrey R. Pavlov,Nadezhda Pavlova,Valeri N. Karamychev,N. N. Polouchine,V. V. Shakhova,Igor V. Grigoriev,Yunian Lou,D. Rohksar,Susan Lucas,Katherine H. Huang,David Goodstein,Trevor Hawkins,V. Plengvidhya,V. Plengvidhya,Dennis L. Welker,Joanne E. Hughes,Yong Jun Goh,Andrew K. Benson,K. A. Baldwin,Ju-Hoon Lee,I. Diaz-Muniz,B. Dosti,Vladimir V. Smeianov,W. Wechter,Ravi D. Barabote,Graciela L. Lorca,Eric Altermann,Rodolphe Barrangou,Balasubramanian Ganesan,Y. Xie,Helen Rawsthorne,Diana I. Tamir,C. Parker,Frederick Breidt,Frederick Breidt,Jeffery R. Broadbent,Robert W. Hutkins,Daniel J. O'Sullivan,J. L. Steele,Gülhan Ünlü,Milton H. Saier,Todd R. Klaenhammer,Paul G. Richardson,Sergei A. Kozyavkin,Bart C. Weimer,David A. Mills +51 more
TL;DR: Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Journal ArticleDOI
IMG: the integrated microbial genomes database and comparative analysis system
Victor M. Markowitz,I-Min A. Chen,Krishna Palaniappan,Ken Chu,Ernest Szeto,Yuri Grechkin,Anna Ratner,Biju Jacob,Jinghua Huang,Peter L. Williams,Marcel Huntemann,Iain Anderson,Konstantinos Mavromatis,Natalia Ivanova,Nikos C. Kyrpides +14 more
TL;DR: The Integrated Microbial Genomes system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context and provides tools and viewers for analyzing and reviewing the annotations of genes and genomes inA comparative context.
Journal ArticleDOI
The genome of the cucumber, Cucumis sativus L.
Sanwen Huang,Ruiqiang Li,Zhonghua Zhang,Li Li,Xingfang Gu,Wei Fan,William J. Lucas,Xiaowu Wang,Bingyan Xie,Peixiang Ni,Yuanyuan Ren,Hongmei Zhu,Jun Li,Kui Lin,Weiwei Jin,Zhangjun Fei,Guangcun Li,Jack E. Staub,Andrzej Kilian,Edwin A. G. van der Vossen,Yang Wu,Jie Guo,Jun He,Zhiqi Jia,Yi Ren,Geng Tian,Yao Lu,Jue Ruan,Wubin Qian,Mingwei Wang,Quanfei Huang,Bo Li,Zhaoling Xuan,Jianjun Cao,Asan,Zhigang Wu,Juanbin Zhang,Qingle Cai,Yinqi Bai,Bowen Zhao,Yonghua Han,Ying Li,Xuefeng Li,Shenhao Wang,Qiuxiang Shi,Shiqiang Liu,Won Kyong Cho,Jae-Yean Kim,Yong Xu,Katarzyna Heller-Uszynska,Han Miao,Zhouchao Cheng,Shengping Zhang,Jian Wu,Yuhong Yang,Houxiang Kang,Man Li,Huiqing Liang,Xiaoli Ren,Zhongbin Shi,Ming Wen,Min Jian,Hailong Yang,Guojie Zhang,Zhentao Yang,Rui Chen,Shifang Liu,Jianwen Li,Lijia Ma,Hui Liu,Yan Zhou,Jing Zhao,Xiaodong Fang,Guoqing Li,Lin Fang,Yingrui Li,Dongyuan Liu,Hongkun Zheng,Yong Zhang,Nan Qin,Zhuo Li,Guohua Yang,Shuang Yang,Lars Bolund,Karsten Kristiansen,Hancheng Zheng,Shaochuan Li,Xiuqing Zhang,Huanming Yang,Jing Wang,Rifei Sun,Zhang Baoxi,Shuzhi Jiang,Jun Wang,Yongchen Du,Songgang Li +95 more
TL;DR: This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.
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