Chapter

String Processing and Information Retrieval

Volume 3772 of the series Lecture Notes in Computer Science pp 360-369

Normalized Similarity of RNA Sequences

  • Rolf BackofenAffiliated withInstitute of Computer Science, Friedrich-Schiller Universität Jena, Jena Center for Bioinformatics
  • , Danny HermelinAffiliated withDepartment of Computer Science, University of Haifa
  • , Gad M. LandauAffiliated withDepartment of Computer Science, University of HaifaDepartment of Computer and Information Science, Polytechnic University
  • , Oren WeimannAffiliated withDepartment of Computer Science, University of Haifa

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Abstract

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.