RNA SECONDARY STRUCTURE PREDICTION USING HIGHLY PARALLEL COMPUTERS

An RNA secondary structure prediction method using a highly parallel c omputer is reported, We focus on finding thermodynamically stable stru ctures of a single-stranded RNA molecule. Our approach is based on a p arallel combinatorial method which calculates the free energy of a mol ecule as the sum of the free energies of all the physically possible h ydrogen bonds, Our parallel algorithm finds many highly stable structu res all at once, while most of the conventional prediction methods fin d only the most stable structure, The important idea in our algorithm is search tree pruning, with dynamic load balancing across the process or elements in a parallel computer. Software toots for visualization a nd classification of secondary structures ave also presented using the sequence of cadang-cadang coconut viroid as an example. Our software system runs on CM-5.