FIGURE 1.
Secondary structure (left) and arc (right) diagrams for (A) a four-strand structure without crossing base pairs, (B) a three-strand structure with crossing base pairs (an H-type pseudoknot motif). VfoldMCPX uses the phantom linkers (shown as three red dots) to connect the RNA strands. In the arc diagrams, RNA sequences are shown as black horizontal lines while base pairs are shown as blue arcs. The crossing arcs indicate the crossing base pairs. Specifically labeled motifs are in black boldface.
