Inverse folding of RNA pseudoknot structures

Gao, James ZM; Li, Linda YM; Reidys, Christian M

This construction may result in duplicate, inconsistent or incompatible structures. Here, a structure is inconsistent if there exists at least one position paired with more than one base, and incompatible if there exists at least one arc not compatible with l i-1 , see Figures 18 Figure 15 Skeleton and its L-graph. We display a skeleton (left) and its L-graph (right). Figure 16 An outline of Cross. For illustration purposes we assume here s = 1. The routines SHADOW, SKELETONBRANCH and SATURATION are depicted. Due to space limitations we only represent a few select motifs and for the same reason only one of the motifs displayed in the first row is extended by one arc (drawn in blue). Furthermore note that only motifs with crossings give rise to nontrivial skeleton-trees, all other motifs are considered directly as input for SATURATION. and 19. Here compatibility is understood with respect to the Watson-Crick and G-U base pairing rules. Deleting inconsistent and incompatible structures, as well as those identical to the target, we arrive at the set of competitors,