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/ Oxford University Press

A computational procedure for assessing the significance of RNA secondary structure

Jih-H. Chen 1, Shu-Yun Le , Bruce Shapiro , Kathleen M. Currey and Jacob V. Maizel

Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis, National Cancer Institute, National Institutes of Health Bldg. 469, Rm, 151, Frederick, MD 21701
1Advanced Scientific Computing Laboratory, Program Resources, Inc. NCI/FCRF, Frederick, MD 21701, USA

In our recent series of papers, we have used the structures of statistical significance from Monte Carlo simulations to improve the predictions of secondary structure of RNA and to analyze the possible role of locally significant structures in the ljfe cycle of human immunodeficiency virus. Because of intensive computational requirements for Monte Carlo simulation, it becomes impractical even using a supercomputer to assess the significance of a structure with a window size > 200 along an RNA sequence of 1000 bases or more. In this paper, we have developed a new procedure that drastically reduces the time needed to assess the significance of structures. In fact, the efficiency of this new method allows us to assess structures on the VAX as well as the CRAY

Received on May 11, 1989; accepted on August 22, 1989

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