Normalized Similarity of RNA Sequences

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.

• Type: Conference
• Year: 2005
• Where: SPIRE
• Authors: Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann
• Keywords: Local Similarity Measure, Maximum Normalized Score, Normalized Version, SPIRE 2005