Explorer MOSAIC

Background: The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Description: Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and noncoding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. Conclusion: The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic. Background The increasing number of publicly available, completely sequenced bacterial genomes provides an opportunity for original comparative genomics approaches, especially at short-term evolutionary scales. During the last decade, several algorithms have been developed to respond to the challenging task of aligning whole genomes at the nucleotide level (see, for instance, references [1-3], and [4]). Some algorithms, such as MGA, are limited to collinear genomes [1]. Others, however, such as the MAUVE aligner Published: 27 November 2008 BMC Bioinformatics 2008, 9:498 doi:10.1186/1471-2105-9-498 Received: 11 September 2008 Accepted: 27 November 2008 This article is available from: http://www.biomedcentral.com/1471-2105/9/498 © 2008 Chiapello et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC Bioinformatics 2008, 9:498 http://www.biomedcentral.com/1471-2105/9/498