Edit distance between two RNA structures

Authors:
Guo-Hui Lin;Bin Ma;Kaizhong Zhang
Affiliations:
Department of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada and Department of Computing and Software, McMaster University;Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B7, Canada;Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B7, Canada
Venue:
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Year:
2001

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Abstract

Arc-annotated sequences are useful in representiug the structural information of RNA sequences. Typically, RNA secondary and tertiary structures could be represented by a set of nested arcs and a set of crossing arcs, respectively. As the specified RNA functions are determined by the specified molecular confirmation and therefore the specified secondary and tertiary structures, the comparison between RNA secondary and tertiary structures have received much attention recently. In this paper, we propose the notion of edit distance to measure the similarity between two RNA secondary and tertiary structures, by incorporating the various edit operations performing on both bases and arcs (base-pairs). Several algorithms are presented to compute the edit distance two RNA sequences with various arc structures and under various score schemes, either exactly or approximately. Preliminary experimental tests confirm that our definition of edit distance and the computation model are among the most reasonable ones ever studied in the literature.