A new algorithm for computing similarity between RNA 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 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. (C) 2001 Elsevier Science Inc. All rights reserved.