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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Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Paul J. Kersey,James E. Allen,Alexis Allot,Matthieu Barba,Sanjay Boddu,Bruce J. Bolt,Denise Carvalho-Silva,Mikkel B. Christensen,Paul Davis,Christoph Grabmueller,Navin Kumar,Zicheng Liu,Thomas Maurel,Ben Moore,Mark D. McDowall,Uma Maheswari,Guy Naamati,Victoria L. Newman,Chuang Kee Ong,Michael Paulini,Helder Pedro,Emily Perry,Matthew Russell,Helen Sparrow,Electra Tapanari,Kieron Taylor,Alessandro Vullo,Gareth Williams,Amonida Zadissia,Andrew Olson,Joshua C. Stein,Sharon Wei,Marcela K. Tello-Ruiz,Doreen Ware,Doreen Ware,Aurelien Luciani,Simon C. Potter,Robert D. Finn,Martin Urban,Kim E. Hammond-Kosack,Dan Bolser,Nishadi De Silva,Kevin L. Howe,Nicholas Langridge,Gareth Maslen,Daniel M. Staines,Andrew D. Yates +46 more
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes resource, with a focus on recent developments and expansions, including the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data.
Journal ArticleDOI
The Ensembl Automatic Gene Annotation System
Val Curwen,Eduardo Eyras,T. Daniel Andrews,Laura Clarke,Emmanuel Mongin,Steven M.J. Searle,Michele Clamp +6 more
TL;DR: The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes and annotates genes based on evidence derived from known protein, cDNA, and EST sequences.
Journal ArticleDOI
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection
Jinghua Yang,Dongyuan Liu,Xiaowu Wang,Changmian Ji,Feng Cheng,Baoning Liu,Zhongyuan Hu,Sheng Chen,Deepak Pental,Youhui Ju,Pu Yao,Xuming Li,Kun Xie,Jianhui Zhang,Jianlin Wang,Fan Liu,Weiwei Ma,Jannat Shopan,Hongkun Zheng,Sally A. Mackenzie,Mingfang Zhang +20 more
TL;DR: An allopolyploid Brassica juncea genome was assembled by shotgun and single-molecule reads integrated to genomic and genetic maps and it was discovered that the A subgenomes of B.juncea and Brassica napus each had independent origins.
Journal ArticleDOI
Draft genome of the kiwifruit Actinidia chinensis
Shengxiong Huang,Shengxiong Huang,Jian Ding,Dejing Deng,Wei Tang,Honghe Sun,Dongyuan Liu,Lei Zhang,Xiangli Niu,Xia Zhang,Meng Meng,J. Yu,Jia Liu,Yi Han,Wei Shi,Danfeng Zhang,Shuqing Cao,Zhaojun Wei,Yongliang Cui,Yanhua Xia,Huaping Zeng,Kan Bao,Lin Lin,Ya Min,Hua Zhang,Min Miao,Min Miao,Xiaofeng Tang,Xiaofeng Tang,Yunye Zhu,Yuan Sui,Guangwei Li,Hanju Sun,Junyang Yue,Jiaqi Sun,Fangfang Liu,Liangqiang Zhou,Lin Lei,Xiaoqin Zheng,Ming Liu,Long Huang,Jun Song,Chunhua Xu,Jiewei Li,Kaiyu Ye,Silin Zhong,Silin Zhong,Bao-Rong Lu,Guanghua He,Fangming Xiao,Hui-Li Wang,Hongkun Zheng,Zhangjun Fei,Zhangjun Fei,Yongsheng Liu,Yongsheng Liu +55 more
TL;DR: As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.
Journal ArticleDOI
Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
Ki Joong Kim,Hae Lim Lee +1 more
TL;DR: Through the detailed comparisons of several chloroplast genomes, evolutionary hotspots predominated by the inversion end points, indel mutation events, and high frequencies of base substitutions were identified.
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