Publicação
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
| dc.contributor.author | Vale, Filipa F. | |
| dc.contributor.author | Encarnação, P. | |
| dc.contributor.author | Vítor, Jorge M. B. | |
| dc.date.accessioned | 2025-08-14T16:46:25Z | |
| dc.date.available | 2025-08-14T16:46:25Z | |
| dc.date.issued | 2007-12-16 | |
| dc.date.updated | 2024-03-19T12:00:55Z | |
| 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 Supplementary information: Supplementary data are available at Bioinformatics online. | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | 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. | pt_PT |
| dc.identifier.doi | 10.1093/bioinformatics/btm621 | pt_PT |
| dc.identifier.issn | 1367-4811 | |
| dc.identifier.issn | 1367-4803 | |
| dc.identifier.slug | cv-prod-38679 | |
| dc.identifier.uri | http://hdl.handle.net/10400.5/102916 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.publisher | Oxford University Press | pt_PT |
| dc.relation.publisherversion | https://academic.oup.com/bioinformatics/article/24/3/383/255190 | pt_PT |
| dc.title | A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case | pt_PT |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.citation.endPage | 388 | pt_PT |
| oaire.citation.issue | 3 | pt_PT |
| oaire.citation.startPage | 383 | pt_PT |
| oaire.citation.title | Bioinformatics | pt_PT |
| oaire.citation.volume | 24 | pt_PT |
| person.familyName | Vale | |
| person.familyName | Vítor | |
| person.givenName | Filipa | |
| person.givenName | Jorge | |
| person.identifier.ciencia-id | 4718-00EF-4BF0 | |
| person.identifier.ciencia-id | FF19-99F4-3964 | |
| person.identifier.orcid | 0000-0003-4635-0105 | |
| person.identifier.orcid | 0000-0001-6486-3444 | |
| person.identifier.rid | C-3570-2013 | |
| person.identifier.rid | M-3279-2013 | |
| person.identifier.scopus-author-id | 17136133700 | |
| person.identifier.scopus-author-id | 7801493621 | |
| rcaap.cv.cienciaid | FF19-99F4-3964 | Jorge Manuel Barreto Vítor | |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | article | pt_PT |
| relation.isAuthorOfPublication | b2d398b3-1980-4cc0-9905-9e478bdb85a9 | |
| relation.isAuthorOfPublication | be15e90f-9cc9-4ad0-b9fd-465236b72e9a | |
| relation.isAuthorOfPublication.latestForDiscovery | b2d398b3-1980-4cc0-9905-9e478bdb85a9 |