Edit distance between two RNA structures

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Edit distance between two RNA structures
The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the four-letter alphabet fA; C; G; Ug. 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. Ó 2001 Elsevier Science Inc. All rights rese...
Guohui Lin, Bin Ma, Kaizhong Zhang
Added 30 Jul 2010
Updated 30 Jul 2010
Type Conference
Year 2001
Authors Guohui Lin, Bin Ma, Kaizhong Zhang
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