FIGURE 1.
Three types of graphs representing (A) RNA secondary and (B) RNA tertiary structures. In a cord graph, arcs connect bases that are paired. In a frame graph, telescoping picture frames connect paired bases. In a terrace graph, junctions (or loops) are visualized as flat terraces supported on top of pillars representing the two strands that make up the duplex bounding the junction. The terraces on the right are color-coded to match the junction sequences on the frame diagrams in the center. Tertiary contacts are represented by frames on the lower half plane in a frame diagram, and by rainbow arcs in a terrace diagram.
