title: MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.
abstract: 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. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations.
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France vallenet@genoscope.cns.fr.
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Calteau
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gachet
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lajus
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Josso
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Mercier
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Renaux
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Johan
authors.initials: J
authors.lastname: Rollin
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: Zoe
authors.initials: Z
authors.lastname: Rouy
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France.
authors.forename: David
authors.initials: D
authors.lastname: Roche
authors.affiliation: CEA, Institut de Génomique - Genoscope, Laboratoire d'Informatique Scientifique, F-91000 Évry, France.
authors.forename: Claude
authors.initials: C
authors.lastname: Scarpelli
authors.affiliation: UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France cmedigue@genoscope.cns.fr.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics*; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D012984:Software