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Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http:\/\/progenomes.embl.de\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz1002","type":"journal-article","created":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T11:11:15Z","timestamp":1571397075000},"source":"Crossref","is-referenced-by-count":48,"title":["proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6831-4557","authenticated-orcid":false,"given":"Daniel R","family":"Mende","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivica","family":"Letunic","sequence":"additional","affiliation":[{"name":"Biobyte solutions GmbH, Bothestr, 142, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oleksandr M","family":"Maistrenko","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas S B","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessio","family":"Milanese","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucas","family":"Paoli","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Hern\u00e1ndez-Plaza","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarc\u00f3n, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Askarbek N","family":"Orakov","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sofia K","family":"Forslund","sequence":"additional","affiliation":[{"name":"Max Delbr\u00fcck Centre for Molecular Medicine, 13125 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shinichi","family":"Sunagawa","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georg","family":"Zeller","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaime","family":"Huerta-Cepas","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarc\u00f3n, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luis Pedro","family":"Coelho","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany"},{"name":"Max Delbr\u00fcck Centre for Molecular Medicine, 13125 Berlin, Germany"},{"name":"Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany"},{"name":"Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, 97074 W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,24]]},"reference":[{"key":"2019102405394587000_B1","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1242\/jeb.001370","article-title":"Advanced sequencing technologies and their wider impact in microbiology","volume":"210","author":"Hall","year":"2007","journal-title":"J. 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