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dc.contributor.authorBrilli, Matteoen
dc.contributor.authorMengoni, Alessioen
dc.contributor.authorFondi, Marcoen
dc.contributor.authorBazzicalupo, Marcoen
dc.contributor.authorLio, Pietroen
dc.contributor.authorFani, Renatoen
dc.date.accessioned2011-06-16T16:23:06Z
dc.date.available2011-06-16T16:23:06Z
dc.date.issued2008-12-21en
dc.identifier.citationBMC Bioinformatics 2008, 9:551
dc.identifier.issn1471-2105
dc.identifier.urihttp://www.dspace.cam.ac.uk/handle/1810/237931
dc.description.abstractAbstract Background Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses. Results To overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps. Conclusion The tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins. The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.
dc.languageEnglishen
dc.language.isoen
dc.titleAnalysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Networken
dc.typeArticle
dc.date.updated2011-06-16T16:23:06Z
dc.description.versionRIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.en
dc.rights.holderBrilli et al.; licensee BioMed Central Ltd.
prism.publicationDate2008en
dcterms.dateAccepted2008-12-21en
rioxxterms.versionofrecord10.1186/1471-2105-9-551en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2008-12-21en
dc.contributor.orcidLio, Pietro [0000-0002-0540-5053]
dc.identifier.eissn1471-2105
rioxxterms.typeJournal Article/Reviewen


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