Mende Daniel R, Letunic Ivica, Huerta-Cepas Jaime, Li Simone S, Forslund Kristoffer, Sunagawa Shinichi, Bork Peer
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.
Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. doi: 10.1093/nar/gkw989. Epub 2016 Oct 24.
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.
微生物基因组的可得性为微生物学开辟了许多新的研究途径。这主要是由比较基因组学方法推动的，该方法依赖于对基因组序列进行准确和一致的表征。然而，对于特定的原核生物进化枝，很难获得一致的分类学和综合功能注释。因此，我们开发了proGenomes，这是一种资源，可让用户方便地访问目前的25038个高质量基因组，其序列和一致的注释可以单独检索，也可以按分类学进化枝检索。根据先前建立的方法，这些基因组被分配到5306个一致且准确的分类学物种簇中。proGenomes还包含近8000万个蛋白质编码基因的功能信息，包括一套全面的通用注释以及针对碳水化合物活性酶和抗生素抗性基因的更具针对性的注释。此外，还为许多基因组提供了广泛的栖息地信息。所有基因组和相关信息都可以通过用户选择的进化枝或多套特定栖息地的代表性基因组进行下载。我们预计，具有全面功能注释的高质量基因组的可得性将推动临床微生物基因组学、功能进化及微生物学其他子领域的进展。proGenomes可在http://progenomes.embl.de获取。
