In the Side Panel of normal sequence views (), you will find an extra group under Nucleotide info called Secondary Structure. This is used to display a symbolic representation of the secondary structure along the sequence (see figure 24.19).
The following options can be set:
- Show all structures. If more than one structure is predicted, this option can be used if all the structures should be displayed.
- Show first. If not all structures are shown, this can be used to determine the number of structures to be shown.
- Sort by. When you select to display e.g. four out of
eight structures, this option determines which the "first four"
- Sort by G.
- Sort by name.
- Sort by time of creation.
- Base pair symbol. How a base pair should be represented (see figure 24.19).
- Unpaired symbol. How bases which are not part of a base pair should be represented (see figure 24.19).
- Height. When you zoom out, this option determines the height of the symbols as shown in figure 24.20 (when zoomed in, there is no need for specifying the height).
- Base pair probability. See Probability-based coloring).