An algorithm for comparing multiple RNA secondary structures

A new distributed computational procedure is presented for rapidlydetermining the similarity of multiple conformations of RNAsecondary structures. A data abstraction scheme is utilizedto reduce the quantity of data that must be handled to determinethe degree of similarity among multiple structures. The methodhas been used to compare 200 structures with easy visualizationof both those structures and substructures that are similarand those that are vastly different. It has the capability ofprocessing many more conformations as a function of researchrequirements. The algorithm is described as well as some suggestionsfor future uses and extensions. Received on October 29, 1987; accepted on May 4, 1988