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.