Abstract
The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base-pairs (nucleotide pairs) which forms bonds between A - U and C - G. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers a notion of similarity between two RNA molecule structures taking into account the primary, the secondary and the tertiary structures. We show that in general this problem is NP-hard for tertiary structures. We present algorithms for the case where at least one of the RNA involved is of secondary structures. We then show that this algorithm might be used to deal with the practical application. We also show an approximation algorithm.
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