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© 1988 IRL Press Ltd

A program for predicting significant RNA secondary structures

Shu-yun Le 1, Jih-Hsiang Chen 2, Kathleen M. Currey and Jacob V. Maizel, Jr

Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis, National Cancer Institute, National Institutes of Health Frederick, MD 21701, USA
1Shanghai Institute of Biochemistry, Chinese Academy of Sciences Shanghai 200031, China
2Advanced Scientific Computer Laboratory Program Resources, Inc. NCI/FCRF, Frederick, MD 21701, USA

We describe a program for the analysis of RNA secondary structure. There are two new features in this program. (i) To get vector speeds on a vector pipeline machine (such as Cray X-MP/24) we have vectorized the secondary structure dynamic algorithm. (ii) The statistical significance of a locally ‘optimal’ secondary structure is assessed by a Monte Carlo method. The results can be depicted graphically including profiles of the stability of local secondary structures and the distribution of the potentially significant secondary structures in the RNA molecules. Interesting regions where both the potentially significant secondary structures and ‘open’ structures (single-stranded coils) occur can be identified by the plots mentioned above. Furthermore, the speed of the vectorized code allows repeated Monte Carlo simulations with different overlapping window sizes. Thus, the optimal size of the significant secondary structure occurring in the interesting region can be assessed by repeating the Monte Carlo simulation. The power of the program is demonstrated in the analysis of local secondary structures of human T-cell lymphotrophic virus type III (HIV).

Received on August 17, 1987; accepted on January 5, 1988

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