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Double String Tandem Repeats

Authors Amihood Amir, Ayelet Butman, Gad M. Landau, Shoshana Marcus, Dina Sokol

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Author Details

Amihood Amir
  • Department of Computer Science, Bar Ilan University, Ramat-Gan, 52900, Israel
Ayelet Butman
  • Department of Computer Science, Holon Institude of Technology, Golomb St 52, Holon, 5810201, Israel
Gad M. Landau
  • Department of Computer Science, University of Haifa, Haifa 31905, Israel
  • NYU Tandon School of Engineering, New York University, Six MetroTech Center, Brooklyn, NY 11201, USA
Shoshana Marcus
  • Department of Mathematics and Computer Science, Kingsborough Community College of the City University of New York, 2001 Oriental Boulevard, Brooklyn, NY 11235, USA
Dina Sokol
  • Department of Computer and Information Science, Brooklyn College and The Graduate Center, City University of New York, Brooklyn, NY, USA

Cite AsGet BibTex

Amihood Amir, Ayelet Butman, Gad M. Landau, Shoshana Marcus, and Dina Sokol. Double String Tandem Repeats. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 3:1-3:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


A tandem repeat is an occurrence of two adjacent identical substrings. In this paper, we introduce the notion of a double string, which consists of two parallel strings, and we study the problem of locating all tandem repeats in a double string. The problem introduced here has applications beyond actual double strings, as we illustrate by solving two different problems with the algorithm of the double string tandem repeats problem. The first problem is that of finding all corner-sharing tandems in a 2-dimensional text, defined by Apostolico and Brimkov. The second problem is that of finding all scaled tandem repeats in a 1d text, where a scaled tandem repeat is defined as a string UU' such that U' is discrete scale of U. In addition to the algorithms for exact tandem repeats, we also present algorithms that solve the problem in the inexact sense, allowing up to k mismatches. We believe that this framework will open a new perspective for other problems in the future.

Subject Classification

ACM Subject Classification
  • Theory of computation → Design and analysis of algorithms
  • Theory of computation → Pattern matching
  • double string
  • tandem repeat
  • 2-dimensional
  • scale


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