MicroScope: a platform for microbial genome annotation and comparative genomics.
MicroScope: a platform for microbial genome annotation and comparative genomics.
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DOI：
10.1093/database/bap021
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Médigue C
中科院分区：
文献类型：
--
作者：
Vallenet D;Engelen S;Mornico D;Cruveiller S;Fleury L;Lajus A;Rouy Z;Roche D;Salvignol G;Scarpelli C;Médigue C
基因组测序的最初结果是创建以四个字母表书写的长文本字符串。计算机序列分析的作用是帮助生物学家将生物学知识与这些序列联系起来，使研究人员能够做出可以通过实验进行测试的推断和预测。科学界有各种各样的软件可供使用，并可用于在预测其生物功能之前识别基因组对象。然而，只有有限数量的生物学上有趣的功能可以从一个孤立的序列。另一方面，比较基因组学工具通过同时汇集众多基因组中包含的信息，允许注释者基于进化和自然选择是所有生物过程定义的核心的想法进行推断。我们开发了MicroScope平台，以便为微生物基因组注释和比较分析的系统和有效修订提供基于网络的框架（http：//www.genoscope.cns.fr/agc/microscope）。从MicroScope管道中实现的注释过程的流程图的描述，以及传统和新型微生物注释和比较分析工具的开发开始，本文强调了专家注释作为自动注释的补充的重要作用。几个例子说明了使用实施工具的审查和管理的注释的新的和公开的微生物基因组内MicroScope的丰富的综合基因组框架。该平台被用作浏览器，以浏览现有微生物基因组（迄今为止超过440种生物）的最新注释信息，并在新注释项目（117种细菌基因组）的背景下。MicroScope数据库中收集的人类专业知识（约280，000个独立注释）有助于提高微生物基因组注释的质量，特别是对于最初仅通过自动程序分析的基因组。数据库URL：http://www.genoscope.cns.fr/agc/mage和http://www.genoscope.cns.fr/agc/microcyc
The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone. Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc
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影响因子：
14.9
作者：
Klimke W;Agarwala R;Badretdin A;Chetvernin S;Ciufo S;Fedorov B;Kiryutin B;O'Neill K;Resch W;Resenchuk S;Schafer S;Tolstoy I;Tatusova T
通讯作者：
Tatusova T
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
14.9
作者：
Lima T;Auchincloss AH;Coudert E;Keller G;Michoud K;Rivoire C;Bulliard V;de Castro E;Lachaize C;Baratin D;Phan I;Bougueleret L;Bairoch A
通讯作者：
Bairoch A
DOI：
10.1007/bf00266910
发表时间：
1978-01-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
MATSUMOTO, H;OHTA, S;TERAWAKI, Y
通讯作者：
TERAWAKI, Y