title: Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops.
abstract: 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 strain-specific sequences called loops.
  
  
  RESULTS
  Here, we generalize this approach and propose a strategy that allows systematic and non-biased 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 documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops.
  
  
  CONCLUSIONS
  The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.
authors: Mathématique, Informatique & Génome, INRA Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France. helene.chiapello@jouy.inra.fr
authors: H
authors: H
authors: Chiapello
authors: I
authors: I
authors: Bourgait
authors: F
authors: F
authors: Sourivong
authors: G
authors: G
authors: Heuclin
authors: A
authors: A
authors: Gendrault-Jacquemard
authors: M-A
authors: MA
authors: Petit
authors: M
authors: M
authors: El Karoui
mesh_terms: D016960:Agrobacterium tumefaciens / Q000145:classification; D001409:Bacillus cereus / Q000145:classification; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D016993:Chlamydophila pneumoniae / Q000145:classification; D002874:Chromosome Mapping / Q000295:instrumentation; D017124:Conserved Sequence; D030541:Databases, Genetic; D004926:Escherichia coli / Q000145:classification; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics*; D007256:Information Systems / Q000458:organization & administration; D020407:Internet; D016415:Sequence Alignment; D013045:Species Specificity