MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis
Résumé
1 Introduction
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, the
LABGeM group at Genoscope has developed the MicroScope platform (https://www.genoscope.
cns.fr/agc/microscope) which 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. MicroScope serves different use cases in bioinformatics:
— it supports the integration of newly sequenced or already available prokaryotic genomes through
the offer of a free-of-charge service to the scientific community
— it performs computational inferences including prediction of gene function, metabolic pathways,
resistome and virulome
— it provides tools for comparative genomics and metabolic analyses
— it supports collaborative expert annotation and community-based curation efforts in a rich
comparative genomics context through the use of specific curation tools and graphical interfaces.
MicroScope contains data for ∼ 10,000 microbial genomes, which are manually curated and analyzed
by microbiologists (> 4,000 personal accounts in January 2019).
2 Contributions
The platform has been under continuous development since 2006 [1,2]. We will present an overview
of the MicroScope analysis pipelines and illustrate the use of several new functionalities which concern:
— automatic annotation based on the UniRule system
— annotation of virulence and antimicrobial resistance genes
— comparative genomics with synteny computations and pan-genome analyses
— prediction and characterization of regions of genomic plasticity like secretion systems, integrons
and secondary metabolite biosynthesis gene clusters
— metabolic network reconstruction
References
[1] Claudine M´edigue, Alexandra Calteau, St´ephane Cruveiller, Mathieu Gachet, Guillaume Gautreau, Adrien
Josso, Aur´elie Lajus, Jordan Langlois, Hugo Pereira, R´emi Planel, David Roche, Johan Rollin, Zoe Rouy,
and David Vallenet. MicroScope—an integrated resource for community expertise of gene functions and
comparative analysis of microbial genomic and metabolic data. Briefings in Bioinformatics, sep 2017.
[2] Adrien Josso, Alexandra Calteau, Alexandre Renaux, Aur´elie Lajus, David Roche, Johan Rollin, Jonathan
Mercier, Mathieu Gachet, St´ephane Cruveiller, Zoe Rouy, Claudine M´edigue, David Vallenet, and Claude
Scarpelli. MicroScope in 2017: an expanding and evolving integrated resource for community expertise of
microbial genomes. Nucleic Acids Research, 45(D1):D517–D528, nov 2016.
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