Secondary Structure plot and Dot plot

The ``dot plot'' in test_dp.ps shows the pair probabilities within the equilibrium ensemble as $n\times n$ matrix, and is an excellent way to visualize structural alternatives. A square at row $i$ and column $j$ indicates a base pair. The area of a square in the upper right half of the matrix is proportional to the probability of the base pair $(i,j)$ within the equilibrium ensemble. The lower left half shows all pairs belonging to the MFE structure. While the MFE consists of a single helix, three helices are visualized in the pair probabilities.

Next, let's use the relplot utility to visualize which parts of a predicted MFE are well-defined and thus more reliable. Also let's use a real example for a change and produce yet another representation of the predicted structure, the mountain plot.