EXAMPLE 3

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EXAMPLE 3

Here we present some results from the folding of an RNA that is related to a Human adenovirus pre-terminal protein (U52533). This RNA exhibits both ``well-defined'' and ``poorly-defined'' folding regions, as shown in Figure 17. A total of 7 foldings were computed using the default parameters.


  
Figure 17: The energy dot plot for the ``Example 3'' sequence, with ΔG = -196.3 kcal/mol and ΔΔG = 9.8 kcal/mol. The region from bases 180 to 295 shows a great deal of uncertainty in its folding. This may be interpreted as a large ensemble of different foldings, or simply an ``unstructured'' region. In contrast, the long stem pairing bases 160-178 with 316-298, respectively, is extremely well determined. Also well-determined is a stem loop region that stretches from 37-81 and 322-365.
  \begin{figure}\epsfig{file=Example3.ps,width=\textwidth} \end{figure}


Michael Zuker
Center for Computational Biology
Washington University in St. Louis
1998-12-05