CCZhong_rnaCrossingAlignment

CCZhong_rnaCrossingAlignment - General RNA structural edit...

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General RNA structural edit distance problem Cun-cong Zhong
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Background What is RNA? Why study RNA? Why study RNA structures? Why edit distance? A-U, C-G
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Formulation Given two RNA structures, compute the minimum number of operations needed to change one structure to another The operation allowed are: Relabeling a base-pair Inserting a base-pair Deleting a base-pair
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Background In terms of this problem What is a RNA structure? Secondary: a set of nested parentheses Tertiary: a set of pairwise interactions, not necessarily nested A dynamic programming algorithm for the nested case
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Data
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Formulation An optimization problem Given two RNA structures, and an integer k, can we use less than k allowed operations to change one structure to another?
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Proving NP-completeness This is a decision problem The answer can be verified in polynomial time: The oracle gives us the k steps Can be verified in polynomial time
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CCZhong_rnaCrossingAlignment - General RNA structural edit...

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