SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances. Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny bloc...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Frédéric Lemoine, Bernard Labedan, Olivier Lespinet
• Keywords: BMCBI 2008, Genomes, Large Number, Synteny Blocks