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Fixed-parameter tractable sampling for RNA design with multiple target structures

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Academic year: 2021

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Figure 1 General outline of RNARedPrint. From a set of target secondary structures (i), base pairs are merged (ii) into a (base pair) dependency graph (iii) and transformed into a tree
Figure 2 Toy example of a tree decomposition associated with two target structures in the stacking energy model (where the four positions of each base pair stack depend on each other).
Figure 3 Comparison of free energy and Boltzmann probability for 10 000 uniform (π = 1; blue dots) and Boltzmann distributed (π = 500; green dots) sequences, targeting a simple structure consisting of two adjacent helices.
Figure 4 A fitted energy model based on stacking pairs (A) leads to approximated free-energies that are highly correlated (R=0.99) with free-energies in the Turner energy model (B), yet induces tree widths that are amenable to practical sampling (C).
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