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© IRL Press Ltd

An algorithm for comparing multiple RNA secondary structures

Bruce A. Shapiro

Image Processing Section, Laboratory of Mathematical Biology, Frederick Cancer Research Facility Building 469, Room 150, Frederick, MD 21701, USA

A new distributed computational procedure is presented for rapidly determining the similarity of multiple conformations of RNA secondary structures. A data abstraction scheme is utilized to reduce the quantity of data that must be handled to determine the degree of similarity among multiple structures. The method has been used to compare 200 structures with easy visualization of both those structures and substructures that are similar and those that are vastly different. It has the capability of processing many more conformations as a function of research requirements. The algorithm is described as well as some suggestions for future uses and extensions.

Received on October 29, 1987; accepted on May 4, 1988

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