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DOI: 10.4230/LIPIcs.CPM.2020.3

Double String Tandem Repeats

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

Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

Abstract

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.

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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)

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@InProceedings{amir_et_al:LIPIcs.CPM.2020.3,
  author =	{Amir, Amihood and Butman, Ayelet and Landau, Gad M. and Marcus, Shoshana and Sokol, Dina},
  title =	{{Double String Tandem Repeats}},
  booktitle =	{31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)},
  pages =	{3:1--3:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-149-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{161},
  editor =	{G{\o}rtz, Inge Li and Weimann, Oren},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.3},
  URN =		{urn:nbn:de:0030-drops-121283},
  doi =		{10.4230/LIPIcs.CPM.2020.3},
  annote =	{Keywords: double string, tandem repeat, 2-dimensional, scale}
}

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Double String Tandem Repeats

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