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A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
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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.
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.
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Citação
Vale 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.
Editora
Oxford University Press