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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. June 2004, Volume 3, Number 6, 361-367

Identifying the Largest Common Substructure of RNA Structures
Bo Liao and Tian-ming Wang
Internet Electron. J. Mol. Des. 2004, 3, 361-367

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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 structure of an RNA is a set of free bases and base pairs formed 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 largest common substructure (LCS) between two RNA molecule structures taking into account the primary and the secondary structures. We present a dynamic programming algorithm for identifying the largest common substructure of two RNA structures. The proposed algorithm solve the LCS problem in time O(mn).

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