Fast and Adaptive Variable Order Markov Chain Construction

  • Marcel H. Schulz
  • David Weese
  • Tobias Rausch
  • Andreas Döring
  • Knut Reinert
  • Martin Vingron
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5251)


Variable order Markov chains (VOMCs) are a flexible class of models that extend the well-known Markov chains. They have been applied to a variety of problems in computational biology, e.g. protein family classification. A linear time and space construction algorithm has been published in 2000 by Apostolico and Bejerano. However, neither a report of the actual running time nor an implementation of it have been published since. In this paper we use the lazy suffix tree and the enhanced suffix array to improve upon the algorithm of Apostolico and Bejerano. We introduce a new software which is orders of magnitude faster than current tools for building VOMCs, and is suitable for large scale sequence analysis.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Marcel H. Schulz
    • 1
    • 3
  • David Weese
    • 2
  • Tobias Rausch
    • 2
    • 3
  • Andreas Döring
    • 2
  • Knut Reinert
    • 2
  • Martin Vingron
    • 1
  1. 1.Department of Computational Molecular BiologyMax Planck Institute for Molecular GeneticsBerlinGermany
  2. 2.Department of Computer ScienceFree University of BerlinBerlinGermany
  3. 3.International Max Planck Research School for Computational Biology and Scientific Computing 

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