Tree Representation of RNA

In the tree representation, each vertex of tree represents a base pair in the secondary structure, while each directed edge represents that the end of the knot (a base pair ) is itself interior to the start of the knot (a base pair ). The exterior base pair of a cycle will lead to exactly vertices under this configuration.

A lot of information is lost in the tree representation, yet it represents the simplest possible way to represent an RNA structure. Furthermore, every base pair can be assigned an order in this representation. Every terminal vertex is assigned the label . For any vertex . that has outgoing edges, let be the maximum order of vertices that had incoming edges from . If occurs exactly once, also has the order . However if appears more than once is assigned the order .