MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis - Archive ouverte HAL Accéder directement au contenu
Poster De Conférence Année : 2021

MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

Résumé

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. 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://mage.genoscope.cns.fr/microscope) [1]. The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts. Launched in 2005, the platform has been under continuous development within the LABGeM team at Genoscope. 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, we integrated several tools to analyze a wide range of biological systems (antibiotic resistance, virulence, secondary metabolites, integrons, secretions systems, CRISPR-Cas clusters…). Particularly, tools from the PPanGGOLiN software suite (https://github.com/labgem/PPanGGOLiN) allows users to analyze pangenomes from several hundreds of genomes of the same species and to explore their content in regions of genomic plasticity [2,3]. The platform also has extensive functionality to explore and compare metabolic pathways. MicroScope 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 >14,500 microbial genomes, part of which are manually curated and maintained by microbiologists (>5,400 user accounts in March 2021). The platform is also a useful resource for academic training. This poster gives an overview of the platform and its evolution and presents new methodologies and tools already integrated or currently being developed. Acknowledgements This work was supported in part by FRANCE GENOMIQUE [ANR-10-INBS-09–08] and INSTITUT FRANÇAIS DE BIOINFORMATIQUE [ANR-11-INBS-0013]. References 1. David Vallenet, Alexandra Calteau, Mathieu Dubois et al. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Research, Jan 8;48(D1):D579-D589, 2020. 2. Guillaume Gautreau, Adelme Bazin, Mathieu Gachet et al. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Computational Biology, Mar 19;16(3):e1007732, 2020. 3. Adelme Bazin, Guillaume Gautreau, Claudine Médigue et al. panRGP: a pangenome-based method to predict genomic islands and explore their diversity. Bioinformatics, Dec 30;36(Suppl_2):i651-i658, 2020.
Fichier non déposé

Dates et versions

hal-04360241 , version 1 (21-12-2023)

Identifiants

  • HAL Id : hal-04360241 , version 1

Citer

Alexandra Calteau, Mathieu Dubois, Jérôme Arnoux, Adelme Bazin, Mylène Beuvin, et al.. MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France. ⟨hal-04360241⟩
16 Consultations
0 Téléchargements

Partager

Gmail Facebook X LinkedIn More