title: MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.
abstract: 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.
  
  
  METHODS
  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 non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons.
  
  
  CONCLUSIONS
  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.
authors.affiliation: INRA UR1077, Unité Mathématique, Informatique & Génome, Domaine de Vilvert, 78352, Jouy-en-Josas, France. helene.chiapello@jouy.inra.fr
authors.forename: Hélène
authors.initials: H
authors.lastname: Chiapello
authors.forename: Annie
authors.initials: A
authors.lastname: Gendrault
authors.forename: Christophe
authors.initials: C
authors.lastname: Caron
authors.forename: Jérome
authors.initials: J
authors.lastname: Blum
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Petit
authors.forename: Meriem
authors.initials: M
authors.lastname: El Karoui
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics; D003628:Database Management Systems; D030541:Databases, Genetic; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D020407:Internet; D014584:User-Computer Interface