GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

Background: Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results: To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M- GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M- GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 ( containing 75 cloned genomes from a set of 15 published enterobacterial genomes) in an hour. M- GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion: M- GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M- GCAT is freely available for download for academic and non- commercial use at: http:// alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.