The Circles , Domes , DotPlot , Mountains , and Squiggles programs accept the FoldRNA output file and graph the RNA secondary structure. Circles , Domes , DotPlot , and Mountains make abstract representations, but the graphs they draw are easier to compare if you are looking for secondary structure motifs.
Mountains makes a graph that looks like a mountain range.
Horizontal striations upon a particular peak are bonds between bases, and vertical links between the horizontal striations represent stems. To make your graph more readable, you can suppress the base labels and decrease horizontal density to create multipage plots. Circles , Domes , Mountains , DotPlot , and Squiggles all make graphic secondary structure representations with the .connect output file from FoldRNA . The stems can be plotted with DotPlot . The secondary structures of large molecules may make crowded graphs.