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© 1985 IRL Press Ltd.

Computer program for prediction of the optimal and suboptimal secondary structures of long RNA molecules

K. Yamamoto and H. Yoshikura

Department of Bacteriology, Faculty of Medicine, University of Tokyo 7–3–1 Hongo, Bunyo–ku, Tokyo, Japan

We present an algorithm for prediction of RNA secondary structures. The program consists of three parts: the first computes location and free energy of every possible stem–loop structure, the second computes probability of its formation, and the third lists the positions and free energies of all the stem–loops in the order of their probability sizes. The circular RNA molecule of chrysanthemum stunt viroid was used as an input data for demonstrating the operation of the program.

Received on March 14, 1985; accepted on March 18, 1985

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