Searching for gapped palindromes

  • Authors:
  • Roman Kolpakov;Gregory Kucherov

  • Affiliations:
  • Moscow University, Russia;LIFL and INRIA Lille - Nord Europe, Lille, France and J.-V.Poncelet Lab., Moscow, Russia

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2009

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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 each of the two classes, we propose an algorithm that runs in time O(n+S) for a constant-size alphabet, where S is the number of output palindromes. Both algorithms can be extended to compute biological gapped palindromes within the same time bound.