Publicação
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
| dc.contributor.author | Vítor, Jorge Manuel Barreto | |
| dc.contributor.author | Encarnação, P. | |
| dc.contributor.author | Vale, Filipa | |
| dc.date.accessioned | 2013-08-28T13:56:00Z | |
| dc.date.available | 2013-08-28T13:56:00Z | |
| dc.date.issued | 2008 | |
| dc.date.updated | 2011-11-18T09:34:28Z | |
| dc.description | © The Author 2007. Published by Oxford University Press. All rights reserved. | |
| dc.description.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 | por |
| dc.identifier.citation | Vítor, Jorge Manuel Barreto; Encarnação, P.; Vale, Filipa. A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case, Bioinformatics, 24, 3, 383-388, 2008. | por |
| dc.identifier.issn | 1367-4803 | |
| dc.identifier.uri | http://dx.doi.org/10.1093/bioinformatics/btm621 | |
| dc.identifier.uri | http://hdl.handle.net/10451/9041 | |
| dc.language.iso | eng | por |
| dc.peerreviewed | yes | por |
| dc.relation.publisherversion | http://bioinformatics.oxfordjournals.org/content/24/3/383 | por |
| dc.title | A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case | por |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.citation.endPage | 388 | por |
| oaire.citation.startPage | 383 | por |
| oaire.citation.title | Bioinformatics | por |
| oaire.citation.volume | 24 | por |
| rcaap.rights | restrictedAccess | por |
| rcaap.type | article | por |