EXAMPLE 1

The energy dot plot is an integral part of the folding prediction. Consider the folding of a short RNA sequence:
ACCCCCUCCU UCCUUGGAUC AAGGGGCUCA A,
using default parameters. $\Delta G= -9.8$ kcal/mole at 37$^{\circ}$, so $\Delta \Delta G= 1.0$ rather than 5% of $\Delta G$. A single, optimal folding is computed. A glance of the energy dot plot , shown in Figure 13, reveals the optimal folding in black dots (symbols), but another set of yellow dots, indicating base pairs in at least 1 other suboptimal folding. The default value of `W' (2, from Table 3) is too large for this other folding to be predicted, but a glance at the dot plot shows that something else is there. When the sequence is refolded with `W'=0, a second, totally different folding is predicted. Figure 14 displays these foldings with individual bases drawn.

  

Figure 13: The energy dot plot for the ``Example 1'' sequence. Surrounding annotation, which would not be legible at this scale, has been removed. The yellow dots indicate base pairs in foldings within 0.3 kcal/mole of the optimal folding free energy of -9.8 kcal/mole.

  

Figure 14: The 2 predicted foldings for the ``Example 1'' sequence. (a) The optimal folding with $\Delta G= -9.8$kcal/mole. (b) The suboptimal fold ( $\Delta G= -9.5$ kcal/mole) found after refolding with `W'=0.