Fig. 2

An example of a connected component of the dependency graph. a An example of the set of three targets T1, T2, and T3. Nucleotide positions are numbered above the example, e.g, shadowed columns from the left to the right correspond to nucleotide positions 1, 9, 13, 21, 25, 33, 37, 42, respectively. As an example, base paired positions belonging to a connected component are shadowed. The dependency graph is composed of all connected components (not shown except the shadowed one) derived from the targets. b A graph representation of the connected component shadowed in (a). The numbers indicate nucleotide positions. An edge corresponds to a base pair between nucleotide positions. If there is a base pair in one of the target structures, an edge appears in a connected component. E.g., nucleotide positions 21 and 25 in a have a base pair in T3, so that there is an edge between node 21 and 25 in (b). c Decomposition of the connected component into the paths, where a cycle is treated as a path by defining a single vertex as a ‘start and end’ vertex (e.g. the cycle shown at the left of this figure). The start and end vertices are denoted by solid circles