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. 2017 Jan 4;45(D1):D210-D218.
doi: 10.1093/nar/gkw934. Epub 2016 Oct 18.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

David M Kristensen  1   2 , Yuri I Wolf  2 , Eugene V Koonin  2
Affiliations

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

David M Kristensen et al. Nucleic Acids Res. .

Abstract

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html.

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Figures

Figure 1.
Figure 1.
Distribution of archaeal and bacterial taxa in the Aligned Tight Genomic Clusters (ATGCs). (A) multidimensional chart showing taxa with more members as wider slices and those represented in more ATGCs as greater distance from the center. (B) Stacked area plot showing ATGC size.
Figure 2.
Figure 2.
The ATGC data set webpage. A user can choose an individual ATGC to find more information about it (link in left-most column), or use the provided information to choose a set of ATGCs for large-scale analyses. The color scheme was chosen to match that of the most current version of the COG database (blue, bacteria; orange, archaea), with links provided to organisms appearing in both databases in the ‘COGs’ column (middle of table).
Figure 3.
Figure 3.
An individual ATGC webpage. The page provides descriptive information about the ATGC, as well as about each genomic assembly in the group and the pangenomic distribution of genes shared across multiple genomes. Clicking the name of an individual genome assembly (right-most column of the table) takes the user to a page containing all of the proteins in that genome and additional data for each, such as the ATGC-COG membership, genomic coordinates, various known gene names and symbols and other information.
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References

    1. Novichkov P.S., Ratnere I., Wolf Y.I., Koonin E.V., Dubchak I. ATGC: A database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res. 2009;37:D448–D454. - PMC - PubMed
    1. Novichkov P.S., Wolf Y.I., Dubchak I., Koonin E.V. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J. Bacteriol. 2009;191:65–73. - PMC - PubMed
    1. Kristensen D.M., Kannan L., Coleman M.K., Wolf Y.I., Sorokin A., Koonin E.V., Mushegian A. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010;26:1481–1487. - PMC - PubMed
    1. Tatusov R.L., Koonin E.V., Lipman D.J. A genomic perspective on protein families. Science. 1997;278:631–637. - PubMed
    1. Koonin E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 2005;39:309–338. - PubMed

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