Vale, Filipa F.Encarnação, P.Vítor, Jorge M. B.2025-08-142025-08-142007-12-16Vale FF, Encarnação P, Vítor JMB. A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case. Bioinformatics 2008;24:383–8. https://academic.oup.com/bioinformatics/article/24/3/383/255190.1367-48111367-4803http://hdl.handle.net/10400.5/102916Motivation: 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. 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. Availability: The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip Supplementary information: Supplementary data are available at Bioinformatics online.engjournal article2024-03-19cv-prod-3867910.1093/bioinformatics/btm621