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MicroScope: a platform for microbial genome annotation and comparative genomics

机译：MicroScope：微生物基因组注释和比较基因组学的平台

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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
机译：基因组测序的最初结果是创建了以四个字母组成的长文本字符串。计算机序列分析的作用是协助生物学家将生物学知识与这些序列相关联，从而使研究者能够做出可以通过实验进行检验的推断和预测。科学界可以使用各种软件，并且可以在预测基因组对象的生物学功能之前，先对其进行识别。然而，从分离的序列中只能揭示出有限数量的生物学上有趣的特征。另一方面，比较基因组学工具通过同时收集众多基因组中包含的信息，使注释者可以基于进化和自然选择对所有生物过程的定义至关重要的思想进行推断。我们已经开发了MicroScope平台，以提供一个基于Web的框架，用于系统有效地修改微生物基因组注释和比较分析（http://www.genoscope.cns.fr/agc/microscope）。从对MicroScope管道中实现的注释过程的流程图的描述，以及传统和新颖的微生物注释和比较分析工具的开发开始，本文强调专家注释作为自动注释的补充的基本作用。几个示例说明了在MicroScope丰富的集成基因组框架内，如何使用已实现的工具来审查和管理新的和可公开获得的微生物基因组的注释。该平台用作查看器，以浏览可用的微生物基因组（迄今已有440多种生物）的更新注释信息，以及在新注释项目（117个细菌基因组）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进行分析的基因组。数据库网址：http://www.genoscope.cns.fr/agc/mage和http://www.genoscope.cns.fr/agc/microcyc

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