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...

• Type: Conference
• Year: 2001
• Where: RECOMB
• Authors: Guohui Lin, Bin Ma, Kaizhong Zhang
• Keywords: Four-letter Alphabet FA, RECOMB 2001, RNA Molecule Structures, Tertiary Structures