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Communication Dans Un Congrès Année : 2018

"MicroScope: an integrated platform for the annotation and exploration of microbial gene functions using genomic and metabolic comparative analysis"

Résumé

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. The LABGeM team, located at the French sequencing centre (Genoscope, Evry), focuses its research activities on the development and application of new methods for the functional annotation of gene functions. These tools are then made available through MicroScope (http://www.genoscope.cns.fr/agc/microscope), an integrated platform dedicated to microbial genome annotation and comparative analysis, which is developed in our group since more than 14 years. The resource provides data from complete and ongoing genome projects together with post-genomic experiments (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections) allowing users to improve the understanding of gene functions. With more than 3800 user accounts (70% being held by scientists outside of France) and about 800 citations, the MicroScope platform has reached a high impact. Today, MicroScope contains data for more than 9,300 microbial genomes, of which ∼3600 are publicly available. Part of these genomes are manually curated and maintained by biologists. Here I will give an overview of the MicroScope platform components (workflow analysis, database and web interface) and illustrate the use of some functionalities useful in the context of data discovery and expert annotation of biological functions. A focus will be made on (comparative) tools recently integrated in the platform, such as the prediction of virulence and resistance genes, and the prediction of gene clusters involved in secondary metabolites biosynthesis.
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Dates et versions

hal-04367514 , version 1 (03-01-2024)

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  • HAL Id : hal-04367514 , version 1

Citer

Claudine Médigue. "MicroScope: an integrated platform for the annotation and exploration of microbial gene functions using genomic and metabolic comparative analysis". Conference "Marine Flavobacteria ", INRAE (E. Duchaud) au Centre CNRS de Cargèse, Jun 2018, Cargèse (Corse), France. ⟨hal-04367514⟩
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