Structure output

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].