proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
| Autor: | Anthony Fullam, Ivica Letunic, Thomas S B Schmidt, Quinten R Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R Mende |
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| Přispěvatelé: | Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, 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. |
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: | |
| Zdroj: | Nucleic acids research, 51(D1), D760-D766. Oxford University Press Nucleic Acids Research, 51 (D1) |
| ISSN: | 0305-1048 |
| Popis: | 7 Pág. 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/. Amsterdam UMC; European Molecular Biology Laboratory (EMBL); Swiss National Science Foundation (SNSF) [205321_184955 to S.S.]; NCCR Microbiomes [51NF40_180575 to S.S. and C.v.M.]; German Federal Ministry of Education and Research (BMBF); de.NBI network [031A537B to P.B., 031L0181A to G.Z.]; German Research Foundation (DFG) [395357507 – SFB 1371 to G.Z., ‘NFDI4Microbiota’ to P.B.]; European Grant with code [PGC2018-098073-A-I00MCIU/AEI/FEDER to J.H.-C.]; Spanish Ministry of Universities [FPU-19/06635 to C.S.-L.]. Funding for open access charge: EMBL. |
| Databáze: | OpenAIRE |
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