Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

Background: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strainspecific sequences called loops. Results: Here, we generalize this approach and propose a strategy that allows systematic and nonbiased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of docu...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Hélène Chiapello, I. Bourgait, F. Sourivong, G. Heuclin, Annie Gendrault-Jacquemard, Marie-Agnès Petit, Meriem El Karoui
• Keywords: Bacterial Genomes, BMCBI 2005, Genome Alignments, Genomes