Fig. 1

Sampling dependency examples in RNAdualPF for different structural elements: (a) stacked base pair, (b) hairpin, (c) 1×3 internal loop, (d) 3×3 internal loop and (e) multiloop. Base pair (i,j) to be sampled is highlighted in red, positions whose energy contribution is dependent on the instantiation of (i,j) are highlighted in blue, and positions that are mutually dependent, but independent of the instantiation of (i,j), are highlighted in green. Unpaired positions where the nucleotide choice has no effect in the free energy of the structure are indicated in black