MicroScope – Genoscope – Evry

Posted on février 8, 2010 by

Located at Genoscope – the French National Sequencing Center – our bioinformatic team ( Laboratory of Bioinformatics Analysis in Genomic and Metabolim – LABGeM) has developed the MicroScope platform to support microbial genomes (re)annotation projects and comparative analysis. The platform is RIO/IBiSA labelled since 2006.

The system published in 2006 (Vallenet et al., Nucleic Acids Research 34: 53-65) and 2009 (Vallenet et al., Database 2009:bap021) is composed of three main components: An automatic pipeline which combines a set of syntactic and functional annotation tools to predict genes and their biological functions, Genomic and metabolic databases to store the primary data, the pipeline results and the human-curated annotations, and the metabolic networks, A graphical web interface, Magnifying Genome (MaGe) which is the component accessible to our users, via a secure or a public connection to our Web server. It allows to perform relevant expert annotation to efficiently explore and compare the set of prokaryotic genomes using sophisticated query interface, comparative genomics and metabolomics (phyloprofile), etc.

Services associated with MicroScope are: the complete analysis of the novel genome(s) and *Scope project delivery, a four-day training course (http://www.genoscope.cns.fr/agc/mage/training), updates and maintenance of the MicroScope projects and a continuing support and assistance to MaGe users. The access to the platform is available upon request, with priority given to bacterial genomes being sequenced at Genoscope.

Outline :

People :
5,4 ETP : 4 ingeniors (of which 3 permanent positions) + 1,4 researchers.

Computer resources:
Applications that support the MicroScope platform run concurrently on the Genoscope computing facility. It is currently made of a cluster of 330 cores and 200 To storage.

Hosted databases :
• Public : UniProt, COG, InterPro, KEGG, MetaCyc, ISFinder,…
• Own : PkGDB (Prokaryotic genome database), MicroCyc (PGDBs built with PathwayTool, P Karp, USA)

Annotation pipeline :
• Integrated tools : tRNA-scan, ReepSeek, Blast, COGnitor, InterProScan, Artemis, CGView, Pathologic (from Pathway Tool)
• Developed tools : AMIGene, MICheck, Syntonizer, RGPFinder, SNIPer,…

MaGe graphical interface :
• Expert annotation : Gene editor, keyword interface, …
• Comparative tools : phyloprofile/synteny, metabolic phyloprofile, LinePlot, …

Organisms :
Bacterial genomes (pathogens, environnemental organisms), ‘simple’ procaryotic metagenomes, archae, plasmid, phages.

• 68 MicroScope projects : http://www.cns.fr/agc/mage
• ANR PFTV MicroScope

Information on the MaGe training courses are available at (http://www.genoscope.cns.fr/agc/mage/training)

Web site : MicroScope


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