Working flow of the remove-and-expand algorithm in 2dRNAdca for an RNA (PDB ID: 2KDQ_B). The base pair connected by red lines are the native ones. (a) The bases in the top 0.2L standard co-pairs inferred by mfDCA are in red and green, where L is the length of the RNA. In these co-pairs, there are a single base pair (in red) and two one-to-two base pairs that each includes a base pair connected by a red line and a base pair connected by a green line (non-native base pair). The single base pair and the base pairs connected by red lines in the two one-to-two base pairs can be expanded and are retained after the removing step. (b) The result after the removing step. (c) The expanded result of (b) where the expanded base pairs are in light blue.