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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis
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Edité par CCSD -
International audience. Background:Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Objectives:To address this challenge, we develop the MicroScope platform, which is an integrated Web platform for management, annotation, comparative analysis and visualization of microbial genomes (https://www.genoscope.cns.fr/agc/microscope). Methods:Published for the first time in 2006, the platform has been under continuous development within the LABGeM group at Genoscope and provides analysis for complete and ongoing genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions.We will present an overview of the MicroScope analysis pipelines and illustrate the use of several new functionalities in the context of data discovery and expert annotation, which concern:- automatic annotation by UniFire software based on UniRule system,- annotation of virulence and antimicrobial resistance genes,- comparative genomics with synteny computations and pan-genome analyses,- prediction of regions of genomic plasticity and their characterization, like, secretion systems, integrons and secondary metabolite biosynthesis gene clusters,- and metabolic network reconstruction. Results:To date, MicroScope contains data for >10,000 microbial genomes, part of which are manually curated and maintained by microbiologists (>4,000 personal accounts in January 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.
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