Speeding up the detection of evolutive tandem repeats

  • Authors:

  • Richard Groult;Martine Léonard;Laurent Mouchard

  • Affiliations:

  • LIFAR-ABISS, Faculté des Sciences, Universite de Rouen, 76821 Mont Saint Aignan, Cedex, France;LIFAR-ABISS, Faculté des Sciences, Universite de Rouen, 76821 Mont Saint Aignan, Cedex, France;UMR 6037-ABISS, Faculté des Sciences, Université de Rouen, 76821 Mont Saint Aignan, Cedex, France and Department Computer Science, King's College London, London WC2R 2LS, UK

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2004

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Abstract

We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. MFCS'02: the 27th Internat. Symp. Mathematical Foundations of Computer Science, Warszawa, Otwock, Poland, August 2002, Lecture Notes in Computer Science, Vol. 2420, Springer, Berlin, pp. 292-304) which consist in a series of almost contiguous copies having the following property: the Hamming distance between two consecutive copies is always smaller than a given parameter e. In this article, we present a significative improvement that speeds up the detection of evolutive tandem repeats. It is based on the progressive computation of distances between candidate copies participating to the evolutive tandem repeat. It leads to a new algorithm, still quadratic in the worst case, but much more efficient on average, authorizing larger sequences to be processed.