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Bioinformatics Advance Access originally published online on March 1, 2007
Bioinformatics 2007 23(9):1172-1174; doi:10.1093/bioinformatics/btm070
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Phylogenetic exploration of bacterial genomic rearrangements

Romain Fremez 1, Thomas Faraut 2, Gwennaele Fichant 1, Jérôme Gouzy 3 and Yves Quentin 1,*

1Université Paul Sabatier, CNRS-LMGM, UMR 5100, 118, route de Narbonne, 31062 Toulouse, Cedex, 2Laboratoire de Génétique Cellulaire INRA UMR444 and 3Laboratoire des Interactions Plantes Microorganismes INRA/CNRS UMR441/2594, Chemin de Borde Rouge BP52627 31326 Castanet Tolosan Cedex, France

*To whom correspondence should be addressed.


  Abstract

Summary: We present a graphical tool dedicated to the exploration of bacterial genome rearrangements. The principle of this exploration relies on the reconstruction of ancestral genomes at each internal node of a gene-order-based phylogenetic tree. This tool allows the selection of internal nodes to visualize the rearrangements between the inferred chromosome of this node and its direct descendant on the tree.

Availability: PEGR is available at the Genopole Toulouse Bioinformatics platform.

Supplementary information: Online supplementary data are available at PEGR web site: http://bioinfo.genopole-toulouse.prd.fr/pegr.

Associate Editor: Chris Stoeckert

Received on November 21, 2006; revised on February 16, 2007; accepted on February 22, 2007

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[Abstract] [Full Text] [PDF]


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