Fig. 1.

Examples of CP search for helixes versus EHwDs and EHwDs decomposition heuristic. (a) MFE structure check made for EH on the left, and EHwD on the right. In each line, either a new base pair (2 positions) or a new nucleotide (1 position) is instantiated, following the variable order heuristic. For simplification, this example assumes that correct value assignments are made in each instantiation step. (b) Tree decomposition for target structure S₁ (resp. S₂) at temperature T₁ (resp. T₂), using target structures for the FourU element CP000647.1/1773227-1773291. The table on the right presents the order of helix exploration using overlap₁ and overlap₂ heuristics