Figure 2

Illustration of the triangular inequality property. (a) Triangular inequality property of RNA secondary structure alignment. The horizontal lines indicate RNA sequences A and B. The dashed arcs are the pseudo base pairs added to the specific nucleotides, while the shaded areas define the correspondence between regions that are being aligned. (b) Alternative paths that go through either p^A and p^B, or $p_{\chi }^A$ and $p_{{\chi }^{\prime }}^B$. The two shadings (dark and light gray) along the arcs represent the two alternative paths.