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Symbolic representation in sequence view
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. Different options can be set.
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 the first four.
- Sort by Δ G.
- Sort by name.
- Sort by time of creation.
- Match symbols. How a base pair should be represented.
- No match symbol. How bases which are not part of a base pair should be represented.
- Height. When you zoom out, this option determines the height of the symbols (when zoomed in, there is no need for specifying the height).
- P-optimal values. Colors the symbols according to
P-optimal values .
- Foreground color. Colors the letter using a gradient, where the left side color is used for low values and the right side color is used for high values. The sliders just above the gradient color box can be dragged to highlight relevant levels. The colors can be changed by clicking the box. This will show a list of gradients to choose from.
- Background color. Sets a background color of the residues using a gradient in the same way as described above.
When you zoom in and out, the appearance of the symbols change.
