Normalized Similarity of RNA Sequences

  • Rolf Backofen
  • Danny Hermelin
  • Gad M. Landau
  • Oren Weimann
Conference paper

DOI: 10.1007/11575832_40

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3772)
Cite this paper as:
Backofen R., Hermelin D., Landau G.M., Weimann O. (2005) Normalized Similarity of RNA Sequences. In: Consens M., Navarro G. (eds) String Processing and Information Retrieval. SPIRE 2005. Lecture Notes in Computer Science, vol 3772. Springer, Berlin, Heidelberg

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Rolf Backofen
    • 1
  • Danny Hermelin
    • 2
  • Gad M. Landau
    • 3
    • 4
  • Oren Weimann
    • 2
  1. 1.Institute of Computer ScienceFriedrich-Schiller Universität Jena, Jena Center for BioinformaticsGermany
  2. 2.Department of Computer ScienceUniversity of HaifaIsrael
  3. 3.Department of Computer ScienceUniversity of HaifaHaifaIsrael
  4. 4.Department of Computer and Information SciencePolytechnic UniversityNew YorkUSA

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