Layout of JContextExplorer windows. (A) JContextExplorer operates via usage of an initial data-loading frame, followed by coordination of a main window and multi-genome browser context viewer window (top). These frames have several associated child windows (second row): from the main window, a scrollable list of gene annotations (Annotations) and a window to facilitate multiple loading and switching between alternative context sets (Add/Remove Context Sets); from the context viewer window, an alphabetized gene color legend (Color Legend), and pop-up window of information relating to a specific gene (Gene Information). An enlarged view of the context viewer window (B) reveals a scrollable viewing area, where genes are rendered as colors rectangles appearing above or below a centerline, depending on their strandedness. Genes are colored according to homology or associated annotation. The Gene Information panel (lower left-hand corner) describes information to be delivered upon click (Gene Information window). Toggling checkboxes in the Genome Display panel (lower center) modifies the display of all rendered genomic segments. The range of the displayed region may be easily changed in the Range Around Context Segment panel (lower right-hand corner).