LinearCapR: Linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits (opens in new tab)

AbstractMotivationRNA molecules adopt dynamic ensembles of secondary structures, where the local structural context of each nucleotide–such as whether it resides in a stem or a specific type of loop–strongly shapes molecular interactions and regulatory function. Structural-context probabilities therefore provide a more functionally informative view of RNA folding than the minimum free energy structures or base-pairing probabilities. However, existing tools either require O(N3) time or employ ...