Searching for Gapped Palindromes

  • Roman Kolpakov
  • Gregory Kucherov
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5029)

Abstract

We study the problem of finding, in a given word, all maximal gapped palindromes verifying two types of constraints, that we call long-armed and length-constrained palindromes. For both classes, we propose algorithms that run in time O(n + S), where S is the number of output palindromes. Both algorithms can be extended to compute biological gapped palindromes within the same time bound.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Roman Kolpakov
    • 1
  • Gregory Kucherov
    • 2
  1. 1.Moscow UniversityMoscowRussia
  2. 2.LIFL/CNRS/INRIAParc scientifique de la Haute BorneVilleneuve d’AscqFrance

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