Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

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

Frédéric Lemoine12, Bernard Labedan1* and Olivier Lespinet1

Author Affiliations

1 Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât. 400, 91405 Orsay Cedex, France

2 Laboratoire de Recherche en Informatique, Université Paris Sud XI, CNRS UMR 8623, Bât. 490, 91405 Orsay Cedex, France

For all author emails, please log on.

BMC Bioinformatics 2008, 9:536  doi:10.1186/1471-2105-9-536

Published: 16 December 2008

Abstract

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 blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr webcite.

Conclusion

SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.