A new algorithm for computing similarity between RNA structures

Abstract 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 or tertiary structure of an RNA is a set of base-pairs (nucleotide pairs) which form bonds between A–U and C–G. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. We consider the edit distance between two RNA structures. This is a notion of similarity, introduced in [Proceedings of the Tenth Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, vol. 1645, Springer, Berlin, 1999, p. 281], between two RNA molecule structures taking into account the primary, the secondary and the tertiary structures. In general this problem is NP-hard for tertiary structures. In this paper, we consider this notion under some constraints. We present an algorithm and then show how to use this algorithm for practical applications.

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