Brief Bioinform. 2019 Jul 19;20(4):1071-1084. doi: 10.1093/bib/bbx113.
The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.
每天都有大量新的细菌基因组可供使用，因此准确的基因组注释成为了至关重要的一步，它最终决定了存储在公共数据库中的数千个基因组的相关性。MicroScope 平台（http://www.genoscope.cns.fr/agc/microscope）是一个集成资源，支持系统和高效地修订微生物基因组注释、数据管理和比较分析。从我们的语法、功能和关系注释管道的结果出发，MicroScope 为原核基因组的专家注释和比较分析提供了一个集成的环境。它结合了工具和图形界面，用于分析基因组，并在比较基因组学和代谢背景下对基因功能进行手动整理。在本文中，我们描述了免费的 MicroScope 服务，用于注释和分析微生物（宏）基因组、转录组和重测序数据。然后，以提供实用指导和帮助的方式介绍了平台的功能，帮助非生物信息学专家更好地使用该平台。新集成的分析工具（即细菌基因组中毒力和抗性基因的预测）和最近开发的原始方法（泛基因组图表示）也进行了描述。通过用户社区，像 MicroScope 这样的集成环境显然有助于维护准确的资源。
