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Computing similarity between RNA secondary structures

The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the four-letter alphabet {A,C,G,U}. The secondary structure of an RNA is a set of base-pairs (nucleotide pairs) which formed bonds between A-U and C-G. These bonds have been traditional assumed to be non-crossing in the secondary structure. This implies a tree representation of the secondary structure of RNA molecule. This paper considers several notions of similarity between two RNA molecule structures taking into account both the primary and the secondary structures. We consider a natural tree representation with both primary and secondary structure data. We present efficient algorithms for comparing such tree representation. We then show that some of these similarity notions can be used to solve the structure prediction problem when the structure of a closely related RNA is known.