The predict secondary structure
algorithm always calculates the minimum free energy structure of the input sequence.
In addition to this, it is also possible to compute a sample of suboptimal structures by ticking the checkbox labeled
Compute sample of suboptimal structures
Subsequently, you can specify
how many structures to include in the output. The algorithm then iterates over all permissible canonical
base pairs and computes the minimum free energy and associated
secondary structure constrained to contain a specified base pair.
These structures are then sorted by their minimum free energy and the
most optimal are reported given the specified number of structures.
Note, that two different sub-optimal structures can have the same
minimum free energy. Further information about suboptimal folding can be found in [Zuker, 1989a