Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.
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DOI：
10.1093/nar/gkaa958
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Partensky F
中科院分区：
文献类型：
--
作者：
Garczarek L;Guyet U;Doré H;Farrant GK;Hoebeke M;Brillet-Guéguen L;Bisch A;Ferrieux M;Siltanen J;Corre E;Le Corguillé G;Ratin M;Pitt FD;Ostrowski M;Conan M;Siegel A;Labadie K;Aury JM;Wincker P;Scanlan DJ;Partensky F
Cyanorak v2.1(http://www.sb-roscoff.fr/cyanorak)是一个致力于可视化、比较和管理原氯球菌、聚球藻和蓝藻基因组的信息系统，这些微生物是地球上资源最丰富的光合作用微生物。该数据库包括来自97个基因组的序列，涵盖了这些群体中迄今已知的大部分广泛的遗传多样性，并被分成25,834个可能的同源群体(木偶)聚类。用户界面可以访问基因组特征、登录号以及显示菌株分离地点的交互式地图。数据库的主要条目是通过搜索一个术语(基因名称、产品等)，得到木鞋和单个基因的列表。每个阻塞物都得益于丰富的功能注释，包括蛋酒、EC/K数字、围棋术语、TIGR角色、定制设计的Cyanorak角色以及几个蛋白质基序预测。Cyanorak还显示种系概况，指明每个阻塞的基因和色素类型，以及基因组查看器(JBrowse)，用于可视化每个基因组上的额外数据，如预测的操纵子、基因组岛或转录组数据(如果可用)。该信息系统还包括BLAST搜索工具、比较基因组背景以及各种数据导出选项。总而言之，Cyanorak v2.1是生态相关海洋微生物比较基因组学的无价、可扩展的工具。
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
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影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
12.3
作者：
Dufresne, Alexis;Ostrowski, Martin;Scanlan, David J.;Garczarek, Laurence;Mazard, Sophie;Palenik, Brian P.;Paulsen, Ian T.;de Marsac, Nicole Tandeau;Wincker, Patrick;Dossat, Carole;Ferriera, Steve;Johnson, Justin;Post, Anton F.;Hess, Wolfgang R.;Partensky, Frederic
通讯作者：
Partensky, Frederic
影响因子：
14.9
作者：
Fujisawa T;Narikawa R;Maeda SI;Watanabe S;Kanesaki Y;Kobayashi K;Nomata J;Hanaoka M;Watanabe M;Ehira S;Suzuki E;Awai K;Nakamura Y
通讯作者：
Nakamura Y
DOI：
10.1073/pnas.1717069115
发表时间：
2018-02-27
影响因子：
11.1
作者：
Grebert, Theophile;Dore, Hugo;Garczarek, Laurence
通讯作者：
Garczarek, Laurence
影响因子：
7.4
作者：
Blot, Nicolas;Mella-Flores, Daniella;Garczarek, Laurence
通讯作者：
Garczarek, Laurence