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Nucleic Acids Research, 1989, Vol. 17, No. 12 4829-4845
© 1989

MOLECULAR BIOLOGY

Detection of common motifs in RNA secondary structures

Hanah Margalit, Bruce A. Shapiro1, Amos B. Oppenheim2 and Jacob V. Maizel, Jr1

Laboratory of Mathematical Biology, National Cancer Institute, National Institutes of Health Bethesda, MD 20892 1Frederick Cancer Research Facility Frederick, MD 21701, USA 2Department of Molecular Genetics, Hebrew University, Hadassah Medical School Jerusalem 91010, Israel

Received January 9, 1989. Revised May 19, 1989. Accepted May 19, 1989.

We describe a novel computerized system for comparison of RNA secondary structures and demonstrate its use for experimental studies. The system is able to screen a very large number of structures, to cluster similar structures and to detect specific structural motifs. In particular, the system is useful for detecting mutations with specific structural effects anong all possible point mutations, and for predicting compensatory mutations that will restore the wild type structure. The algorithms are independent of the folding rules that are used to generate the secondary structures.


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