Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network |
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Authors: | Matteo Brilli Alessio Mengoni Marco Fondi Marco Bazzicalupo Pietro Liò Renato Fani |
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Institution: | (1) Department of Evolutionary Biology, University of Florence, via Romana 17, I-50125 Florence, Italy;(2) Computer Laboratory, University of Cambridge, 15 JJ Thompson Avenue, Cambridge, CB3 0FD, UK;(3) Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Lyon, France |
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Abstract: | 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. |
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