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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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>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<jats:italic>Escherichia<\/jats:italic>,<jats:italic>Salmonella<\/jats:italic>and<jats:italic>Shigella<\/jats:italic>spps.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>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<jats:italic>Escherichia<\/jats:italic>,<jats:italic>Salmonella<\/jats:italic>and<jats:italic>Shigella<\/jats:italic>plasmids and to focus on possible roles of unannotated proteins.<\/jats:p><jats:p>The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-9-551","type":"journal-article","created":{"date-parts":[[2008,12,23]],"date-time":"2008-12-23T07:13:37Z","timestamp":1230016417000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network"],"prefix":"10.1186","volume":"9","author":[{"given":"Matteo","family":"Brilli","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessio","family":"Mengoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Fondi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Bazzicalupo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Li\u00f2","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renato","family":"Fani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,12,21]]},"reference":[{"key":"2536_CR1","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.plasmid.2004.06.006","volume":"52","author":"MW Gilmour","year":"2004","unstructured":"Gilmour MW, Thomson NR, Sanders M, Parkhill J, Taylor DE: The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics. 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