{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T21:51:17Z","timestamp":1718747477892},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in genome evolution and their implications for the study of biological systems. Detection of conserved regions (descending from a common ancestor) not only helps clarify genome evolution but also makes it possible to identify quantitative trait loci (QTLs) and investigate gene function.<\/jats:p>\n            <jats:p>The identification and comparison of conserved regions on a genome scale is computationally intensive, making process automation essential. Three key requirements are necessary: consideration of phylogeny to identify orthologs between multiple species, frequent updating of the annotation and panel of compared genomes and computation of statistical tests to assess the significance of identified conserved gene clusters.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a modular system superimposed on a multi-agent framework, called CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution). CASSIOPE automatically identifies statistically significant conserved regions between multiple genomes based on automated phylogenies and statistical testing. Conserved regions were searched for in 19 species and 1,561 hits were found. To our knowledge, CASSIOPE is the first system to date that integrates evolutionary biology-based concepts and fulfills all three key requirements stated above. All results are available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/194.57.197.245\/cassiopeWeb\/displayCluster?clusterId=1\" ext-link-type=\"uri\">http:\/\/194.57.197.245\/cassiopeWeb\/displayCluster?clusterId=1<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions.<\/jats:p>\n            <jats:p>\n              <jats:bold>Source code<\/jats:bold> is freely available, please contact: Pierre.pontarotti@univ-provence.fr<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-284","type":"journal-article","created":{"date-parts":[[2009,9,10]],"date-time":"2009-09-10T18:14:04Z","timestamp":1252606444000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["CASSIOPE: An expert system for conserved regions searches"],"prefix":"10.1186","volume":"10","author":[{"given":"Virginie Lopez","family":"Rascol","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Levasseur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Chabrol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simona","family":"Grusea","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Gouret","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Etienne GJ","family":"Danchin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Pontarotti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,9,10]]},"reference":[{"key":"3014_CR1","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1016\/j.coi.2007.06.009","volume":"19","author":"V Lopez Rascol","year":"2007","unstructured":"Lopez Rascol V, Pontarotti P, Levasseur A: Ancestral animal genomes reconstruction. Curr Opin Immunol 2007, 19: 542\u2013546. 10.1016\/j.coi.2007.06.009","journal-title":"Curr Opin Immunol"},{"key":"3014_CR2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Bio 1990, 215: 403\u2013410.","journal-title":"J Mol Bio"},{"key":"3014_CR3","doi-asserted-by":"publisher","first-page":"i54","DOI":"10.1093\/bioinformatics\/btg1005","volume":"19","author":"M Brudno","year":"2003","unstructured":"Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S: Global alignment: Finding rearrangements during alignment. Bioinformatics 2003, 19: i54\u201362. 10.1093\/bioinformatics\/btg1005","journal-title":"Bioinformatics"},{"key":"3014_CR4","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"ACE Darling","year":"2004","unstructured":"Darling ACE, Mau B, Blattner FR, Perna NT: Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Research 2004, 14: 1394\u20131403. 10.1101\/gr.2289704","journal-title":"Genome Research"},{"key":"3014_CR5","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/1471-2105-7-201","volume":"7","author":"PS Dehal","year":"2006","unstructured":"Dehal PS, Boore JL: A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 2006, 7: 201. 10.1186\/1471-2105-7-201","journal-title":"BMC Bioinformatics"},{"key":"3014_CR6","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkn828","volume":"37","author":"TJP Hubbard","year":"2009","unstructured":"Hubbard TJP, Aken BL, Ayling S, et al.: Ensembl 2009. Nucleic Acids Res 2009, 37: D690-D697. [http:\/\/www.ensembl.org] 10.1093\/nar\/gkn828","journal-title":"Nucleic Acids Res"},{"key":"3014_CR7","first-page":"55","volume-title":"Comparative Genomics","author":"R Hoberman","year":"2004","unstructured":"Hoberman R, Sankoff D, Durand D: The statistical significance of max-gap clusters. Comparative Genomics 2004, 55\u201371."},{"key":"3014_CR8","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1101\/gr.1975204","volume":"14","author":"G Bourque","year":"2004","unstructured":"Bourque G, Pevzner PA, Tesler G: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research 2004, 14: 507\u2013516. 10.1101\/gr.1975204","journal-title":"Genome Research"},{"key":"3014_CR9","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/1471-2105-6-198","volume":"6","author":"P Gouret","year":"2005","unstructured":"Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EGJ: FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatic 2005, 6: 198. [http:\/\/figenix2.up.univ-mrs.fr\/Figenix\/index.jsp] 10.1186\/1471-2105-6-198","journal-title":"BMC Bioinformatic"},{"key":"3014_CR10","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1007\/s00239-004-2648-1","volume":"59","author":"EGJ Danchin","year":"2004","unstructured":"Danchin EGJ, Pontarotti P: Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome. J Mol Evol 2004, 59: 587\u2013597. 10.1007\/s00239-004-2648-1","journal-title":"J Mol Evol"},{"key":"3014_CR11","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/ng855","volume":"31","author":"L Abi-Rached","year":"2002","unstructured":"Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H: Evidence of en bloc duplication in vertebrate genomes. Nat Genet 2002, 31: 100\u2013105. 10.1038\/ng855","journal-title":"Nat Genet"},{"key":"3014_CR12","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1007\/s00251-003-0601-x","volume":"55","author":"A Vienne","year":"2003","unstructured":"Vienne A, Shiina T, Abi-Rached L, Danchin E, Vitiello V, Cartault F, Inoko H, Pontarotti P: Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region. Immunogenetics 2003, 55: 429\u2013436. 10.1007\/s00251-003-0601-x","journal-title":"Immunogenetics"},{"key":"3014_CR13","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1038\/nature03025","volume":"431","author":"O Jaillon","year":"2004","unstructured":"Jaillon O, Aury JM, Brunet F, et al.: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431: 946\u2013957. 10.1038\/nature03025","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-284.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:36:34Z","timestamp":1630445794000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-284"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,9,10]]},"references-count":13,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3014"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-284","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,9,10]]},"assertion":[{"value":"23 February 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"284"}}