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Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. doi: 10.1093/nar/gkw989. Epub 2016 Oct 24.

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

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Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu, HI 96822, USA.
Biobyte solutions GmbH, Bothestrasse 142, 69126 Heidelberg, Germany.
School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney, Australia.
Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany.
Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.


The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at

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