Figure 3

HCNE track configuration page. Up to three HCNE sets from each pairwise comparison can be shown simultaneously. A set is selected by choosing a similarity threshold (for example, 70% identity over 50 alignment columns), and can be further restricted by an arbitrary threshold on HCNE size. Note that HCNEs may be larger than the window size (30 or 50 columns) used to identify them because the procedure that detects HCNEs merges overlapping conserved elements. For each selected set, the user can choose to see HCNE densities, HCNE locations, or both. Density plots for the different sets will be overlaid (Figure 2a), so that the plot for set two is drawn on top of that for set one, and the plot for set three drawn on top of that for set two. If the option to separate densities based on chromosomes in other genomes is used, the browser will attempt to create one density plot for each chromosome (in the other genome) for which there are HCNEs in the displayed region, or within half a sliding window to either side. If the resulting number of plots exceeds the number of plots requested on this configuration page, densities for the chromosomes with least HCNE sequence in this region will be combined into one plot labeled 'other' (Figure 5).