{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T07:29:47Z","timestamp":1776410987943,"version":"3.51.2"},"reference-count":33,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,10,24]],"date-time":"2019-10-24T00:00:00Z","timestamp":1571875200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FRANCE GENOMIQUE","award":["ANR-10-INBS-09\u201308"],"award-info":[{"award-number":["ANR-10-INBS-09\u201308"]}]},{"name":"INSTITUT FRAN\u00c7AIS DE BIOINFORMATIQUE","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}]},{"name":"Universit\u00e9 d'\u00c9vry"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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. Launched in 2005, the MicroScope platform (https:\/\/www.genoscope.cns.fr\/agc\/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for &gt;11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (&gt;4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.<\/jats:p>","DOI":"10.1093\/nar\/gkz926","type":"journal-article","created":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T08:17:03Z","timestamp":1570522623000},"source":"Crossref","is-referenced-by-count":156,"title":["MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6648-0332","authenticated-orcid":false,"given":"David","family":"Vallenet","sequence":"first","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5871-9347","authenticated-orcid":false,"given":"Alexandra","family":"Calteau","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Mathieu","family":"Dubois","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Paul","family":"Amours","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Adelme","family":"Bazin","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Myl\u00e8ne","family":"Beuvin","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Laura","family":"Burlot","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"},{"name":"UMS 3601 IFB-core, CNRS, INRA, INSERM, CEA & INRIA, Genoscope, Evry, 91057,\u00a0France"}]},{"given":"Xavier","family":"Bussell","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"St\u00e9phanie","family":"Fouteau","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Guillaume","family":"Gautreau","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Aur\u00e9lie","family":"Lajus","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Jordan","family":"Langlois","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"R\u00e9mi","family":"Planel","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"David","family":"Roche","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Johan","family":"Rollin","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Zoe","family":"Rouy","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"given":"Valentin","family":"Sabatet","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3905-1054","authenticated-orcid":false,"given":"Claudine","family":"M\u00e9digue","sequence":"additional","affiliation":[{"name":"LABGeM, G\u00e9nomique M\u00e9tabolique, CEA, Genoscope, Institut Fran\u00e7ois Jacob, CNRS, Universit\u00e9 d'\u00c9vry, Universit\u00e9 Paris-Saclay, Evry, 91057,\u00a0France"}]}],"member":"286","published-online":{"date-parts":[[2019,10,24]]},"reference":[{"key":"2019102405394871300_B1","doi-asserted-by":"crossref","first-page":"D802","DOI":"10.1093\/nar\/gkx1011","article-title":"Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species","volume":"46","author":"Kersey","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019102405394871300_B2","doi-asserted-by":"crossref","first-page":"D666","DOI":"10.1093\/nar\/gky901","article-title":"IMG\/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes","volume":"47","author":"Chen","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2019102405394871300_B3","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource 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