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Bioinformatics Advance Access published online on December 16, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm621
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Vale F. F. 1,*, Encarnação P. 1 and Vítor J. M. B. 2

1Engineering Faculty, Portuguese Catholic University, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
2CECF (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Forças Armadas, 1649-003 Lisboa, Portugal

*To whom correspondence should be addressed. Dr. Filipa Vale, E-mail: filipavale{at}fe.ucp.pt


  Abstract

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.

Contact: filipavale{at}fe.ucp.pt

Supplementary information: Supplementary data are available at bioinformatics online.

Associate Editor: Prof. Martin Bishop

Received on October 19, 2007; revised on December 13, 2007; accepted on December 13, 2007

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