proGenomes 2 (Nucleic Acids Res doi: 10.1093/nar/gkz1002) is an update of proGenomes (Nucleic Acids Res doi: 10.1093/nar/gkw989) and provides 87,920 consistently annotated bacterial and archaeal genomes. Taxonomic annotations are provided as species clusters (Mende et al., Nature Methods, 2013) and as NCBI taxonomy. Functional annotations of over 280 million genes are provided as eggNOG orthologous groups (Huerta-Cepas et al., NAR, 2016) and for antibiotic resistance and virulence.
We further provide a set of 40 universal, single-copy genes for each of the genomes (Cicarelli et al., Science. 2006; Sorek et al., Science, 2007) to support phylogenetic studies of the genomes. Additionally, 12,221 representative genomes covering all species clusters are available for direct download and these can be used for the annotation of metagenomics datasets, large scale phylogenetics and other comparative approaches. Within representative genomes, we also provide habitat specific sets.
Previous version of the database is available at the following address: http://progenomes1.embl.de/
proGenomes 2 is free for academic and non-commercial use. For commercial use or customized versions, please contact biobyte solutions GmbH.
We hope you find the database user-friendly and easy to use. However, if you encounter any problems or have questions, please