{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T01:00:53Z","timestamp":1785546053628,"version":"3.56.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":2832,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,1]]},"DOI":"10.1093\/database\/bap021","type":"journal-article","created":{"date-parts":[[2009,11,26]],"date-time":"2009-11-26T05:34:25Z","timestamp":1259213665000},"source":"Crossref","is-referenced-by-count":225,"title":["MicroScope: a platform for microbial genome annotation and comparative genomics"],"prefix":"10.1093","volume":"2009","author":[{"given":"D.","family":"Vallenet","sequence":"first","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Engelen","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Mornico","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Cruveiller","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L.","family":"Fleury","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Lajus","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Z.","family":"Rouy","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Roche","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G.","family":"Salvignol","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Scarpelli","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"M\u00e9digue","sequence":"additional","affiliation":[{"name":"CEA\/DSV\/IG\/Genoscope-CNRS UMR8030, Laboratoire de G\u00e9nomique Comparative (LGC), 2 rue Gaston Cr\u00e9mieux, 91057 Evry Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,11,25]]},"reference":[{"key":"key\n\t\t\t\t20180618203328_B1","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/gb-2007-8-1-102","article-title":"Genome re-annotation: a wiki solution?","volume":"8","author":"Salzberg","year":"2007","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180618203328_B2","doi-asserted-by":"crossref","first-page":"D471","DOI":"10.1093\/nar\/gkn661","article-title":"HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB\/Swiss-Prot","volume":"37","author":"Lima","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B3","doi-asserted-by":"crossref","first-page":"D216","DOI":"10.1093\/nar\/gkn734","article-title":"The National Center for Biotechnology Information's; Protein Clusters Database","volume":"37","author":"Klimke","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B4","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"Overbeek","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B5","doi-asserted-by":"crossref","first-page":"D528","DOI":"10.1093\/nar\/gkm846","article-title":"The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions","volume":"36","author":"Markowitz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B6","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1093\/nar\/gkh615","article-title":"PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences","volume":"32","author":"D'A;scenzo","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B7","doi-asserted-by":"crossref","first-page":"D338","DOI":"10.1093\/nar\/gki047","article-title":"Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation","volume":"33","author":"Winsor","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B8","doi-asserted-by":"crossref","first-page":"D41","DOI":"10.1093\/nar\/gkj164","article-title":"ASAP: a resource for annotating, curating, comparing, and disseminating genomic data","volume":"34","author":"Glasner","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B9","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkn828","article-title":"Ensembl 2009","volume":"37","author":"Hubbard","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B10","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1093\/nar\/gkg148","article-title":"The ERGO genome analysis and discovery system","volume":"31","author":"Overbeek","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B11","doi-asserted-by":"crossref","first-page":"D408","DOI":"10.1093\/nar\/gkn749","article-title":"PEDANT covers all complete RefSeq genomes","volume":"37","author":"Walter","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B12","doi-asserted-by":"crossref","first-page":"2187","DOI":"10.1093\/nar\/gkg312","article-title":"GenDB \u2013 an open source genome annotation system for prokaryote genomes","volume":"31","author":"Meyer","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B13","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1093\/bioinformatics\/bth273","article-title":"A system for automated bacterial (genome) integrated annotation \u2013 SABIA","volume":"20","author":"Almeida","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B14","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1093\/nar\/gkl471","article-title":"AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system","volume":"34","author":"Bryson","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B15","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: protein phylogenetic profiles","volume":"96","author":"Pellegrini","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180618203328_B16","doi-asserted-by":"crossref","first-page":"93","DOI":"10.3233\/ISB-00009","article-title":"Use of contiguity on the chromosome to predict functional coupling","volume":"1","author":"Overbeek","year":"1999","journal-title":"In Silico Biol."},{"key":"key\n\t\t\t\t20180618203328_B17","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.285.5428.751","article-title":"Detecting protein function and protein-protein interactions from genome sequences","volume":"285","author":"Marcotte","year":"1999","journal-title":"Science"},{"key":"key\n\t\t\t\t20180618203328_B18","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1093\/bioinformatics\/btp393","article-title":"IMG ER: a system for microbial genome annotation expert review and curation","volume":"25","author":"Markowitz","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B19","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1093\/nar\/gkj406","article-title":"MaGe: a microbial genome annotation system supported by synteny results","volume":"34","author":"Vallenet","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B20","doi-asserted-by":"crossref","first-page":"5766","DOI":"10.1093\/nar\/gkh910","article-title":"Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium","volume":"32","author":"Barbe","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B21","article-title":"The Universal Protein Resource (UniProt) 2009","author":"Bairoch","year":"2009"},{"key":"key\n\t\t\t\t20180618203328_B22","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B23","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/nar\/28.1.304","article-title":"The ENZYME database in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B24","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1093\/nar\/gkg590","article-title":"AMIGene: Annotation of MIcrobial Genes","volume":"31","author":"Bocs","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B25","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B26","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B27","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkn766","article-title":"Rfam: updates to the RNA families database","volume":"37","author":"Gardner","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B28","doi-asserted-by":"crossref","first-page":"W471","DOI":"10.1093\/nar\/gki498","article-title":"MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes","volume":"33","author":"Cruveiller","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B29","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B30","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkn785","article-title":"InterPro: the integrative protein signature database","volume":"37","author":"Hunter","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B31","doi-asserted-by":"crossref","first-page":"6633","DOI":"10.1093\/nar\/gkg847","article-title":"Enzyme-specific profiles for genome annotation: PRIAM","volume":"31","author":"Claudel-Renard","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B32","first-page":"175","article-title":"A hidden Markov model for predicting transmembrane helices in protein sequences","volume":"6","author":"Sonnhammer","year":"1998","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"key\n\t\t\t\t20180618203328_B33","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","article-title":"Improved prediction of signal peptides: SignalP 3.0","volume":"340","author":"Bendtsen","year":"2004","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20180618203328_B34","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1093\/bioinformatics\/bti057","article-title":"PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis","volume":"21","author":"Gardy","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B35","doi-asserted-by":"crossref","first-page":"S225","DOI":"10.1093\/bioinformatics\/18.suppl_1.S225","article-title":"The Pathway Tools software","volume":"18","author":"Karp","year":"2002","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B36","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B37","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180618203328_B38","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1093\/embo-reports\/kve097","article-title":"Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes","volume":"2","author":"Hacker","year":"2001","journal-title":"EMBO Rep."},{"key":"key\n\t\t\t\t20180618203328_B39","doi-asserted-by":"crossref","first-page":"D623","DOI":"10.1093\/nar\/gkm900","article-title":"The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases","volume":"36","author":"Caspi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B40","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1089\/mcg.2000.5.205","article-title":"MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products","volume":"5","author":"Serres","year":"2000","journal-title":"Microb. Comp. Genomics"},{"key":"key\n\t\t\t\t20180618203328_B41","doi-asserted-by":"crossref","first-page":"D260","DOI":"10.1093\/nar\/gkl1043","article-title":"TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes","volume":"35","author":"Selengut","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B42","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1128\/MMBR.68.3.518-537.2004","article-title":"Determination of the core of a minimal bacterial gene set","volume":"68","author":"Gil","year":"2004","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"key\n\t\t\t\t20180618203328_B43","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1093\/bioinformatics\/btn529","article-title":"Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database","volume":"24","author":"Carver","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618203328_B44","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkn741","article-title":"Database resources of the National Center for Biotechnology Information","volume":"37","author":"Sayers","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618203328_B45","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/BF00266910","article-title":"Chromosomal location of genes participating in the degradation of purines in Pseudomonas aeruginosa","volume":"167","author":"Matsumoto","year":"1978","journal-title":"Mol. Gen. Genet."},{"key":"key\n\t\t\t\t20180618203328_B46","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1128\/JB.01248-07","article-title":"\u2018Candidatus Cloacamonas acidaminovorans\u2019: genome sequence reconstruction provides a first glimpse of a new bacterial division","volume":"190","author":"Pelletier","year":"2008","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20180618203328_B47","doi-asserted-by":"crossref","first-page":"D181","DOI":"10.1093\/nar\/gkj001","article-title":"TCDB: the Transporter Classification Database for membrane transport protein analyses and information","volume":"34","author":"Saier","year":"2006","journal-title":"Nucleic Acids Res."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/bap021\/16728594\/bap021.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T12:25:36Z","timestamp":1739449536000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bap021\/358148"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,1]]},"references-count":47,"URL":"https:\/\/doi.org\/10.1093\/database\/bap021","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2009]]},"published":{"date-parts":[[2009,1,1]]}}}