Move set MS2[resp. MS1] allows the addition or removal or shift [resp. addition, removal] of a single base pair. The MS2 [resp. MS1 ] distance between secondary structures s and t is defined to be the minimum path length to refold s to t, where a move from MS2[resp. MS1 ] is applied in each step. The MS1 distance between s and t is trivially equal to the cardinality of the symmetric difference of s and t, i.e the number of base pairs belonging to one structure but not the other; in contrast, the computation of MS2 distance is highly non-trivial. We describe algorithms to compute the shortest MS2 folding trajectory between any two given RNA secondary structures.

If you use our program or this server for your work, would you please cite:

  1. Amir H. Bayegan, Peter Clote. Minimum length RNA folding trajectories, (Submitted)