Secondary structure prediction can be accessed in the
Selecting sequences for
Toolbox | Classical Sequence Analysis () | RNA Structure ()| Predict Secondary Structure ()
This opens the dialog shown in figure 22.1.
Figure 22.1: Selecting RNA or DNA sequences for structure prediction (DNA is folded as if it were RNA).
If you have selected sequences before choosing the Toolbox action, they are now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements. You can use both DNA and RNA sequences - DNA will be folded as if it were RNA. Click Next to adjust secondary structure prediction parameters. Clicking Next opens the dialog shown in figure 22.2.
Figure 22.2: Adjusting parameters for secondary structure prediction.