Figure 1.

Graphical representations of RNA structures. Secondary structures of P5abc and tRNA(leu) (top row) are represented as both tree (middle) and dual (bottom) graphs. We use corresponding labels S1, S2, etc. for stems and B1, B2, etc. for bulges, loops or junctions; the chain ends (B0) are not represented in dual graphs. In tree graphs, stems are represented as edges or lines (—) and bulges/loops/junctions/chain ends as vertices (◆). In contrast, in dual graphs, bulges/loops/junctions are represented as edges or lines (—) and stems as vertices (◆).