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Open Access Software

CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes

Joe Rokicki1, David Knox13, Robin D Dowell12* and Shelley D Copley1*

Author Affiliations

1 Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder CO, USA

2 BioFrontiers Institute, University of Colorado at Boulder, Boulder CO, USA

3 Computational Biosciences Program, University of Colorado Anschutz Medical Campus, Aurora CO, USA

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BMC Genomics 2014, 15:65  doi:10.1186/1471-2164-15-65

Published: 24 January 2014

Abstract

Background

The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult.

Results

We have developed CodaChrome (http://www.sourceforge.com/p/codachrome webcite), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori.

Conclusion

CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes.