Figure 2

Grammar for "NoDangle" and "OverDangle". The axiom is struct. Alternative productions starting at the same non-terminal are separated by vertical bars. Terminals, b (a single base), r (a region of bases), ε (the empty word) and loc (the position of a neighbored subword), are colored in blue. Green algebra function names, e. g. sadd or hl, help to write the structures as trees, and are used to associate thermodynamic energies with the structures. Magenta colored words beneath non-terminals are filters, e. g. "stackpairing" requires that the two leftmost bases of the substructure can make base pairs with the two rightmost ones. All different secondary structures for a given RNA sequence, i. e. its complete folding space, can be enumerated by parsing the sequence with grammar NoDangle. The grammar is non-ambiguous in the sense that each structure is found exactly once.