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Comparative RNA structure prediction (RSP) and RNA–RNA interaction prediction (RIP). (A) The three main approaches in comparative RSP: 1. Align-then-fold approach; 2. Fold-then-align approach and 3. Sankoff-type approach (alignment and folding simultaneously); (B) The two main approaches in comparative RIP are (i) interaction between two alignments via an individual RIP tool and (ii) interactions obtained from the joint output of multiple individual RIP tools (adapted from [257]).
