Glossary

Basepair edges

The basepair edges of a bonding graph corresponding to an RNA string $s$ are the dashed edges that connect possible base pairs in $s$ ({A, U} and {C, G}). The gray dashed edges in the figure below illustrate the basepair edges associated with $s$ = "UAGCGUGAUCAC". A matching on basepair edges corresponds to a candidate secondary structure of the strand represented by the RNA string.

Basepair edges may also include {U, G} if we choose to model wobble base pairing.