Fig. 2

Chromosomised view of a strain graph for a V. cholerae strain M66 genome. Vibrio species have two chromosomes, which are clearly shown as the two large circles. Proteins found only on chromosome 1 in the are shown as blue nodes, proteins uniquely found on chromosome 2 are shown as red nodes, proteins, where the chromosome cannot be decided as they occur on both chromosomes in the template genomes, are shown as pink nodes in the smallest circle and proteins which cannot be assigned a chromosome as they do not occur in the template genomes would be shown as grey nodes. The protein nodes are connected to their local neighbours on the contigs though black edges and paralogous proteins are connected to each other with grey edges. Contigs from the input genome are hence denoted by nodes connected through black edges and it the chosen attribute based visualisation from Cytoscape [9] clearly shows the two chromosomes as circles and a separate small circle including only the proteins which cannot be placed. In addition here a region including many paralogous proteins connected by grey edges in chromosome 2 can be seen on the lower left part of chromosome 2. This denotes the known integron island of V. cholerae, which introduces a high structural variability between strains and includes multiple paralogous proteins which in this view create the light grey edges to connect paralogs