{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:14:47Z","timestamp":1728360887619},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,3,24]],"date-time":"2005-03-24T00:00:00Z","timestamp":1111622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,3,24]],"date-time":"2005-03-24T00:00:00Z","timestamp":1111622400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Comparative sequence analysis is an effective and increasingly common way to identify <jats:italic>cis<\/jats:italic>-regulatory regions in animal genomes.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of <jats:italic>cis<\/jats:italic>-regulatory regions in animal genomes. All tools and their source code are freely available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/family.caltech.edu\/\">http:\/\/family.caltech.edu\/<\/jats:ext-link>.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-70","type":"journal-article","created":{"date-parts":[[2005,3,25]],"date-time":"2005-03-25T07:16:08Z","timestamp":1111734968000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison"],"prefix":"10.1186","volume":"6","author":[{"given":"C Titus","family":"Brown","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Xie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric H","family":"Davidson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R Andrew","family":"Cameron","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,3,24]]},"reference":[{"issue":"6","key":"395_CR1","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1016\/j.gde.2003.10.001","volume":"13","author":"GM Cooper","year":"2003","unstructured":"Cooper GM, Sidow A: Genomic regulatory regions: insights from comparative sequence analysis. Curr Opin Genet Dev 2003, 13(6):604\u2013610. 10.1016\/j.gde.2003.10.001","journal-title":"Curr Opin Genet Dev"},{"issue":"1","key":"395_CR2","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1006\/dbio.2002.0619","volume":"246","author":"CT Brown","year":"2002","unstructured":"Brown CT, Rust AG, Clarke PJ, Pan Z, Schilstra MJ, De Buysscher T, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H: New computational approaches for analysis of cis-regulatory networks. Dev Biol 2002, 246(1):86\u2013102. 10.1006\/dbio.2002.0619","journal-title":"Dev Biol"},{"issue":"1","key":"395_CR3","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1006\/dbio.2002.0618","volume":"246","author":"CH Yuh","year":"2002","unstructured":"Yuh CH, Brown CT, Livi CB, Rowen L, Clarke PJ, Davidson EH: Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol 2002, 246(1):148\u2013161. 10.1006\/dbio.2002.0618","journal-title":"Dev Biol"},{"issue":"1","key":"395_CR4","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/S0012-1606(03)00032-0","volume":"257","author":"M Kirouac","year":"2003","unstructured":"Kirouac M, Sternberg PW: cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae. Dev Biol 2003, 257(1):85\u2013103. 10.1016\/S0012-1606(03)00032-0","journal-title":"Dev Biol"},{"issue":"17","key":"395_CR5","doi-asserted-by":"publisher","first-page":"4187","DOI":"10.1242\/dev.00611","volume":"130","author":"LA Romano","year":"2003","unstructured":"Romano LA, Wray GA: Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 2003, 130(17):4187\u20134199. 10.1242\/dev.00611","journal-title":"Development"},{"issue":"4","key":"395_CR6","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1016\/j.cell.2004.08.007","volume":"118","author":"TH Leung","year":"2004","unstructured":"Leung TH, Hoffmann A, Baltimore D: One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell 2004, 118(4):453\u2013464. 10.1016\/j.cell.2004.08.007","journal-title":"Cell"},{"issue":"2","key":"395_CR7","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.ydbio.2004.07.008","volume":"274","author":"R Revilla-i-Domingo","year":"2004","unstructured":"Revilla-i-Domingo R, Minokawa T, Davidson EH: R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. Dev Biol 2004, 274(2):438\u2013451. 10.1016\/j.ydbio.2004.07.008","journal-title":"Dev Biol"},{"key":"395_CR8","unstructured":"PyZine online magazine[http:\/\/www.pyzine.com\/Issue006\/index.html]"},{"key":"395_CR9","unstructured":"FamilyRelations Web site[http:\/\/family.caltech.edu\/]"},{"key":"395_CR10","unstructured":"Caltech Cartwheel server, \"Woodward\"[http:\/\/woodward.caltech.edu\/canal\/]"},{"key":"395_CR11","unstructured":"FamilyRelations tutorial[http:\/\/family.caltech.edu\/tutorial\/]"},{"issue":"1\u20132","key":"395_CR12","doi-asserted-by":"publisher","first-page":"GC1","DOI":"10.1016\/0378-1119(95)00714-8","volume":"167","author":"EL Sonnhammer","year":"1995","unstructured":"Sonnhammer EL, Durbin R: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 1995, 167(1\u20132):GC1\u201310. 10.1016\/0378-1119(95)00714-8","journal-title":"Gene"},{"issue":"3","key":"395_CR13","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 Biol 1990, 215(3):403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"J Mol Biol"},{"issue":"1","key":"395_CR14","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1101\/gr.789803","volume":"13","author":"N Bray","year":"2003","unstructured":"Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13(1):97\u2013102. 10.1101\/gr.789803","journal-title":"Genome Res"},{"issue":"4","key":"395_CR15","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1101\/gr.926603","volume":"13","author":"M Brudno","year":"2003","unstructured":"Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13(4):721\u2013731. 10.1101\/gr.926603","journal-title":"Genome Res"},{"issue":"6","key":"395_CR16","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1006\/geno.2002.7018","volume":"80","author":"L Elnitski","year":"2002","unstructured":"Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R: PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 2002, 80(6):681\u2013690. 10.1006\/geno.2002.7018","journal-title":"Genomics"},{"issue":"4","key":"395_CR17","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1101\/gr.10.4.577","volume":"10","author":"S Schwartz","year":"2000","unstructured":"Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker \u2013 a web server for aligning two genomic DNA sequences. Genome Res 2000, 10(4):577\u2013586. 10.1101\/gr.10.4.577","journal-title":"Genome Res"},{"issue":"Web Server","key":"395_CR18","doi-asserted-by":"publisher","first-page":"W273","DOI":"10.1093\/nar\/gkh458","volume":"32","author":"KA Frazer","year":"2004","unstructured":"Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32(Web Server):W273\u2013279.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"395_CR19","doi-asserted-by":"publisher","first-page":"3027","DOI":"10.1093\/nar\/19.11.3027","volume":"19","author":"TM Yi","year":"1991","unstructured":"Yi TM, Walsh K, Schimmel P: Rabbit muscle creatine kinase: genomic cloning, sequencing, and analysis of upstream sequences important for expression in myocytes. Nucleic Acids Res 1991, 19(11):3027\u20133033.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"395_CR20","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268(1):78\u201394. 10.1006\/jmbi.1997.0951","journal-title":"J Mol Biol"},{"issue":"4","key":"395_CR21","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1101\/gr.10.4.511","volume":"10","author":"G Parra","year":"2000","unstructured":"Parra G, Blanco E, Guigo R: GeneID in Drosophila. Genome Res 2000, 10(4):511\u2013515. 10.1101\/gr.10.4.511","journal-title":"Genome Res"},{"issue":"4","key":"395_CR22","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1101\/gr.10.4.523","volume":"10","author":"A Krogh","year":"2000","unstructured":"Krogh A: Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res 2000, 10(4):523\u2013528. 10.1101\/gr.10.4.523","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-70.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-70\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-70.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:09:14Z","timestamp":1728302954000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-70"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,3,24]]},"references-count":22,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["395"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-70","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,3,24]]},"assertion":[{"value":"18 November 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 March 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 March 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"70"}}