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MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis
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National audience. 1. IntroductionLarge-scale genome sequencing projects are producing a vast amount of new information that is completely transforming 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 for microbiologists.To address this challenge, we develop the MicroScope platform, an integrated Web platform for management, annotation, comparative analysis and visualization of microbial genomes (https://mage.genoscope.cns.fr/microscope) [1]. The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts. 2. MethodsLaunched in 2005, the platform has been under continuous development. MicroScope provides analyses for complete and ongoing genome projects together with metabolic network reconstruction and transcriptomic experiments allowing users to improve the understanding of gene functions. Besides automatic functional annotations, several tools allow analyzing a wide range of biological systems (antibiotic resistance, secondary metabolites, secretions systems, defense systems,...). The platform also has extensive functionalities to explore and compare metabolic pathways. Finally, recent functionalities allow users to perform comparative pangenomics on hundreds of genomes of the same species and to explore their content in regions of genomic plasticity. 3. ResultsMicroScope platform is widely used by microbiologists from academia and industry all around the world for collaborative studies and expert annotation. To date, MicroScope contains data for >16,000 microbial genomes, part of which are manually curated and maintained by microbiologists (>6,100 user accounts in May 2022). The platform is also a useful resource for academic training.AcknowledgementsThe France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale de la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for their support of the MicroScope annotation platform.References 1. David Vallenet, Alexandra Calteau, Mathieu Dubois, Paul Amours, Adelme Bazin, Mylène Beuvin, Laura Burlot, Xavier Bussell, Stéphanie Fouteau, Guillaume Gautreau, Aurélie Lajus, Jordan Langlois, Rémi Planel, David Roche, Johan Rollin, Zoe Rouy, Valentin Sabatet and Claudine Médigue. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Research, 48:D579–D589, 2020.
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