RNA sequences and the EDIT ( NESTED , NESTED ) problem

In molecular biology, RNA structure comparison is of great i nterest to help solving problems as different as phylogeny reconstruction, prediction of molecule folding and identification of a function common to a set of molecules. Lin and al. [13] proposed to define a similarity criterion between RNA struc ures using a concept of edit distance. They proved that computing the edit distance is a M x-SNP hardproblem when at least one of the structures is tertiary. Besides, they gave a polynomial algorithm when at le st one of the structures is primary. Until now remained open the question of the existence of an exact polyn omial algorithm for the problemEDIT(NESTED, NESTED). This problem, as shown by Lin and al. [ 13], corresponds to computing the edit distance between two secondary structures. In this paper, we prove that this prob lem isNP-Complete . General Terms: Algorithms Additional

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