Normalized Similarity of RNA Sequences

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We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An \(\mathcal{O}(n^{2}m{\rm lg}m)\) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and nm. This algorithm has the same time complexity as the currently best known global LCS algorithm.