{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T12:00:34Z","timestamp":1759147234056},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems.<\/jats:p>\n               <jats:p>Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.<\/jats:p>\n               <jats:p>Availability: The software files are available at http:\/\/www.ff.ul.pt\/paginas\/jvitor\/Bioinformatics\/MCRM_algorithm.zip<\/jats:p>\n               <jats:p>Contact: \u00a0filipavale@fe.ucp.pt<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm621","type":"journal-article","created":{"date-parts":[[2007,12,18]],"date-time":"2007-12-18T02:01:49Z","timestamp":1197943309000},"page":"383-388","source":"Crossref","is-referenced-by-count":7,"title":["A new algorithm for cluster analysis of genomic methylation: the <i>Helicobacter pylori<\/i> case"],"prefix":"10.1093","volume":"24","author":[{"given":"F.F.","family":"Vale","sequence":"first","affiliation":[{"name":"1 Engineering Faculty, Portuguese Catholic University, Estrada Oct\u00e1vio Pato, 2635-631 Rio de Mouro, Portugal and 2CECF (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. For\u00e7as Armadas, 1649-003 Lisboa, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P.","family":"Encarna\u00e7\u00e3o","sequence":"additional","affiliation":[{"name":"1 Engineering Faculty, Portuguese Catholic University, Estrada Oct\u00e1vio Pato, 2635-631 Rio de Mouro, Portugal and 2CECF (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. For\u00e7as Armadas, 1649-003 Lisboa, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. M. B.","family":"V\u00edtor","sequence":"additional","affiliation":[{"name":"1 Engineering Faculty, Portuguese Catholic University, Estrada Oct\u00e1vio Pato, 2635-631 Rio de Mouro, Portugal and 2CECF (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. 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