Searching for Gapped Palindromes

  • Authors:
  • Roman Kolpakov;Gregory Kucherov

  • Affiliations:
  • Moscow University, Moscow, Russia 119899;LIFL/CNRS/INRIA, Parc scientifique de la Haute Borne, Villeneuve d'Ascq, France 59650

  • Venue:
  • CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
  • Year:
  • 2008

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Abstract

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