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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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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 <jats:italic>E. coli<\/jats:italic> strains and functional characterization of the loops.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>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: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/genome.jouy.inra.fr\/mosaic\">http:\/\/genome.jouy.inra.fr\/mosaic<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-171","type":"journal-article","created":{"date-parts":[[2005,7,13]],"date-time":"2005-07-13T06:41:27Z","timestamp":1121236887000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops"],"prefix":"10.1186","volume":"6","author":[{"given":"H","family":"Chiapello","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I","family":"Bourgait","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F","family":"Sourivong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G","family":"Heuclin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A","family":"Gendrault-Jacquemard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M-A","family":"Petit","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M","family":"El Karoui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,7,12]]},"reference":[{"issue":"6937","key":"496_CR1","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/nature01644","volume":"423","author":"M Kellis","year":"2003","unstructured":"Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. 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