proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
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- Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Ivica Letunic
- Biobyte solutions GmbH , Bothestr. 142, 69117 Heidelberg, Germany
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- Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Quinten R Ducarmon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Supriya Khedkar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Martin Larralde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Oleksandr M Maistrenko
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology & Biogeochemistry , 1797 SZ, ’t Horntje (Texel), Netherlands
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- Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland
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- Alessio Milanese
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics , ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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- Joao Frederico Matias Rodrigues
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland
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- Claudia Sanchis-López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) , Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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- Christian Schudoma
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Damian Szklarczyk
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland
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- Shinichi Sunagawa
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics , ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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- Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) , Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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- Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland
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- Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany
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- Daniel R Mende
- Department of Medical Microbiology, Amsterdam University Medical Centers , Amsterdam, The Netherlands
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説明
<jats:title>Abstract</jats:title> <jats:p>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/</jats:p>
収録刊行物
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- Nucleic Acids Research
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Nucleic Acids Research 51 (D1), D760-D766, 2022-11-21
Oxford University Press (OUP)