Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor

Itai Boneh, Dvir Fried, Adrian Miclăuş, Alexandru Popa

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Hairpin completion is an operation on formal languages that has been inspired by hairpin formation in DNA biochemistry and has many applications especially in DNA computing. Consider s to be a string over the alphabet {A, C, G, T} such that a prefix/suffix of it matches the reversed complement of a substring of s. Then, in a hairpin completion operation the reversed complement of this prefix/suffix is added to the start/end of s forming a new string. In this paper we study two problems related to the hairpin completion. The first problem asks the minimum number of hairpin operations necessary to transform one string into another, number that is called the hairpin completion distance. For this problem we show an algorithm of running time O(n2), where n is the maximum length of the two strings. Our algorithm improves on the algorithm of Manea (TCS 2010), that has running time O(n2 log n). In the minimum distance common hairpin completion ancestor problem we want to find, for two input strings x and y, a string w that minimizes the sum of the hairpin completion distances to x and y. Similarly, we present an algorithm with running time O(n2) that improves by a O(log n) factor the algorithm of Manea (TCS 2010).

Original languageEnglish
Title of host publication34th Annual Symposium on Combinatorial Pattern Matching, CPM 2023
EditorsLaurent Bulteau, Zsuzsanna Liptak
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959772761
DOIs
StatePublished - Jun 2023
Event34th Annual Symposium on Combinatorial Pattern Matching, CPM 2023 - Marne-la-Vallee, France
Duration: 26 Jun 202328 Jun 2023

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume259
ISSN (Print)1868-8969

Conference

Conference34th Annual Symposium on Combinatorial Pattern Matching, CPM 2023
Country/TerritoryFrance
CityMarne-la-Vallee
Period26/06/2328/06/23

Bibliographical note

Publisher Copyright:
© 2023 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

Keywords

  • dynamic programming
  • exact algorithm
  • incremental trees

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