MicroScope: an integrated platform for bacterial genomic & metabolic annotation
17/06/2014 - Room Courtyard Room at 14:00 - External Seminar
Dr Claudine Medigue
(LABGeM Leader - CNRS)
The annotation of genomes from NGS platforms needs to be automated, high-throughput 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 in the French sequencing centre (Genoscope, Evry), focuses its research activities on the development of new tools dedicated to the analysis of metabolic data. These tools are then made available through MicroScope, an integrated platform dedicated to microbial genome annotation in genomic and metabolic contexts, which is developed in our group since more than 12 years. We will present the MicroScope platform http://www.genoscope.cns.fr/agc/microscope), which is made of three main components: analysis pipelines organized via a workflow management system, a relational database for storing and accessing genomic and metabolic data, and Web graphical interfaces. The resource provides data from completed 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. MicroScope combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Today, the resource contains data for >3,400 microbial genomes, of which about 450 are manually curated and maintained by biologists (1,910 personal accounts in June 2014). Since its first publication in January 2006, the system has been continuously extended both in terms of data content and analysis tools (Vallenet et al. Nucleic Acids Res. 41(D1):D636-47, 2013). In the course of the MICROME European project (www.microme.eu), we worked on the development of new MicroScope tools useful to search for candidate genes in the context of enzymatic activities. Then, our presentation will continue on an updated view of previous conducted surveys on orphan enzymes (Sorokina et al., Biology Direct, in revision). Two strategies will be described that may be helpful in rescuing the orphans by simultaneously combining genomic and metabolic contexts over thousands of organisms (Smith et al., PLoS computational biology 8, 5: e1002540.2012) and in finding new activities by the exploration of the enzymatic diversity within protein families (Bastard et al., Nat Chem Biol., 10(1):42-9, 2014). Expert annotations are continuously gathered in the MicroScope database contributing to the improvement of the quality of microbial genomes annotations, and thus to the predicted metabolic networks and models. To enhance this curation process and assist the biologists, we are working on biological data integration combined with logical reasoning to check completeness and consistency of genome knowledge into the MicroScope platform.