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Approximation to the mean curve in the LCS problem

Author

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  • Durringer, Clement
  • Hauser, Raphael
  • Matzinger, Heinrich

Abstract

The problem of sequence comparison via optimal alignments occurs naturally in many areas of applications. The simplest such technique is based on evaluating a score given by the length of a longest common subsequence divided by the average length of the original sequences. In this paper we investigate the expected value of this score when the input sequences are random and their length tends to infinity. The corresponding limit exists but is not known precisely. We derive a theoretical large deviation, convex analysis and Monte Carlo based method to compute a consistent sequence of upper bounds on the unknown limit. An empirical practical version of our method produces promising numerical results.

Suggested Citation

  • Durringer, Clement & Hauser, Raphael & Matzinger, Heinrich, 2008. "Approximation to the mean curve in the LCS problem," Stochastic Processes and their Applications, Elsevier, vol. 118(4), pages 629-648, April.
    • Handle: RePEc:eee:spapps:v:118:y:2008:i:4:p:629-648
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    Cited by:

    1. Stanislaw Barder & Jüri Lember & Heinrich Matzinger & Märt Toots, 2012. "On Suboptimal LCS-alignments for Independent Bernoulli Sequences with Asymmetric Distributions," Methodology and Computing in Applied Probability, Springer, vol. 14(2), pages 357-382, June.

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