Figure 3

The 'Diagram' view. To draw a diagram, first select corresponding OU parameters using the dropdown lists and click the 'Enter' button. In this example n1_4mer:RV, n1_4mer:GRV and n0_4mer:D were selected for the X, Y and Z axes, respectively. Every dot on the dot-plot corresponds to a genomic fragment selected by the sliding window. Dots are spread and coloured in accordance with their values of the selected statistical OU parameters. Information for each dot may be found by one of the following methods: i) information for a dot under the mouse pointed by the mouse is shown in the 'Message' bar; ii) double clicking a dot returns us to the 'Gene map' tab with the corresponding genomic fragment highlighted; iii) framing the dots and clicking the 'Get' button opens a new applet window with the information about all selected regions. In this example the genomic regions of Salmonella typhimurium LT2 (NC_003197) that correspond to horizontally transferred genetic elements were selected (see discussion in the text).