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

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Official URL:https://doi.org/10.1093/nar/gkw989
PubMed:View item in PubMed
Creators Name:Mende, Daniel R and Letunic, Ivica and Huerta-Cepas, Jaime and Li, Simone S and Forslund, Kristoffer and Sunagawa, Shinichi and Bork, P.
Journal Title:Nucleic Acids Research
Journal Abbreviation:Nucleic Acids Res
Page Range:D529-D534
Date:4 January 2017
Keywords:Computational Biology, Genetic Databases, Genome, Genomics, Molecular Sequence Annotation, Prokaryotic Cells, Taxonomic DNA Barcoding, Web Browser
Abstract: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 http://progenomes.embl.de.
Publisher:Oxford University Press (U.K.)
Item Type:Article

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