ProGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Issue Volume 51:Issue D1(2023) (21st November 2022)

• Record Type: Journal Article
• Authors: Fullam, Anthony; Letunic, Ivica; Schmidt, Thomas S B; Ducarmon, Quinten R; Karcher, Nicolai; Khedkar, Supriya; Kuhn, Michael; Larralde, Martin; Maistrenko, Oleksandr M; Malfertheiner, Lukas; Milanese, Alessio; Rodrigues, Joao Frederico Matias; Sanchis-López, Claudia; Schudoma, Christian; Szklarczyk, Damian; Sunagawa, Shinichi; Zeller, Georg; Huerta-Cepas, Jaime; von Mering, Christian; Bork, Peer; Mende, Daniel R
• Is Part Of: Nucleic acids research. Volume 51:Issue D1(2023)
• Page Start: D760
• Page End: D766
• Publication Date: 2022-11-21
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac1078
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/