Figure 1

Screenshot of the VisualTE interface. The interface is divided into three areas: (i) the ‘Data Selection’ panel, (ii) the ‘Graphical Option’ selection header, and (iii) the ‘Graphical Panel’ (the ‘Location on Chromosome’ panel is visible). In the ‘Data Selection’ panel, the entire Arabidopsis thaliana genome and the Helitrons AtREP1, AtREP3 and AtREP5 are selected. The ‘Gene’ and the ‘Only selected TE Superfamily’ items are selected from the ‘Annotations/TE’ option. Each chromosome is represented by four lines. The three first lines correspond respectively to the selected TEs, the genes, and the TE superfamily lines. The last line is a graduated ruler line. The figure shows a popup menu displayed (gray rectangle) when the user clicks on a graphical item (here the gene). The two textfields (Start and End Position) and the ‘Set Positions’ button display the chromosome region between the two entered values. The ‘Zoom In’ (or ‘Zoom Out’) button increases (or decreases) by two fold the width of selected chromosomes. The ‘Global View’ button resizes the graphical view such that the largest chromosome is entirely included in the graphical panel width.