Manual Crumple Explorer

To better understand the way that crumple completely explores the space of secondary structures of a given sequence, here is a manual version that can be used with very short sequences. Every structure begins completely uncertain, with each nucleotide niether single-stranded nor paired. These undecided nucleotides are represented as en-dashes. The crumple algorithm proceeds by listing all partially-determined structures where the next undetermined base has paired, and then the remaining partial structure in which that base is unpaired. And so slowly, dashes become parentheses or dots.

Though each structure is only one pair away from many others, each structure has only one parent, defined implicitly by the algorithm. This turns the whole partial-structure-space into a tree, and standard tree-enumrating procedures may be used.

To play with this slow-but-visual version of crumple, click on any structure that contains undetermined bases (dashes: -) to see the child-structures.

Note that in order to save space (and your clicking finger), partial structures which can only produce a single child are not shown; they are replaced by their only child.

Enter your sequence here:

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