Example 1

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Next: EXAMPLE 2 Up: Sample foldings Previous: Sample foldings

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. ΔG = -9.8 kcal/mol at 37°, so ΔΔG = 1.0 rather than 5% of ΔG. 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.
\begin{figure}\centering \epsfig{file=1_zoom.ps} \end{figure}


  
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.
\begin{figure}\centering \subfigure[]{\epsfig{file=1-again_1_zoom.ps,width=0.3\t... ...\subfigure[]{\epsfig{file=1-again_2_zoom.ps,width=0.3\textwidth} }\end{figure}

next up previous contents
Next: EXAMPLE 2 Up: Sample foldings Previous: Sample foldings
Michael Zuker
Center for Computational Biology
Washington University in St. Louis
1998-12-05