Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue D1, Pages D529-D534Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw989
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Funding
- European Commission MetaCardis project [FP7HEALTH-305312]
- International Human Microbiome Standards Consortium [HEALTH-FP7-2010-261376]
- European Research Council CancerBiome project [268985]
- GALAXY project [668031]
- Novo Nordisk Foundation [NNF14CC0001]
- European Union Horizon research and innovation programme [686070]
- European Molecular Biology Laboratory (EMBL)
- Australian Postgraduate Award
- EMBL Australia International Ph. D. Fellowship
- European Molecular Biology Organization [ALTF 721-2015]
- LTFCOFUND [PCOFUND-GA-2013-609409]
- EMBL
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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 andmore 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 http://progenomes.embl.de.
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