Hierarchical analysis of RNA secondary structures with pseudoknots based on sections
Fig 2
Energy model calculation examples demonstrating local versus global structural considerations.
a) Pseudoknot base pair structure. The yellow bands represent sets of base pairs belonging to a secondary structure, while the red band represents a set of consecutive pseudoknots. Bottom right shows detailed base pair structure in the pseudoknot. b) Pseudoknot connecting sections across multi-loops. The newly formed loop that includes the pseudoknot contains all sections from the connected multi-loops, requiring global rather than local energy calculations.