We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2 m 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 n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren