Double String Tandem Repeats

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

doi:10.4230/LIPIcs.CPM.2020.3

Double String Tandem Repeats

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

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

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 UU0 such that U0 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. 2012 ACM Subject Classification Theory of computation ! Design and analysis of algorithms; Theory of computation ! Pattern matching.

Original language	English
Title of host publication	31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020
Editors	Inge Li Gortz, Oren Weimann
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)	9783959771498
DOIs	https://doi.org/10.4230/LIPIcs.CPM.2020.3
State	Published - 1 Jun 2020
Event	31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020 - Copenhagen, Denmark Duration: 17 Jun 2020 → 19 Jun 2020

Publication series

Name	Leibniz International Proceedings in Informatics, LIPIcs
Volume	161
ISSN (Print)	1868-8969

Conference

Conference	31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020
Country/Territory	Denmark
City	Copenhagen
Period	17/06/20 → 19/06/20

Bibliographical note

Publisher Copyright:
© 2020 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

Funding

Funding Amihood Amir: Partially supported by Grant No. 2018141 from the United States-Israel Binational Science Foundation (BSF) and Israel Science Foundation Grant 1475-18. Gad M. Landau: Partially supported by Grant No. 2018141 from the United States-Israel Binational Science Foundation (BSF) and Israel Science Foundation Grant 1475-18. Dina Sokol: Partially supported by Grant No. 2018141 from the United States-Israel Binational Science Foundation (BSF).

Funders	Funder number
United States-Israel Binational Science Foundation
Israel Science Foundation	1475-18

Keywords

2-dimensional
Double string
Scale
Tandem repeat

Access to Document

10.4230/LIPIcs.CPM.2020.3

Cite this

Amir, A., Butman, A., Landau, G. M., Marcus, S., & Sokol, D. (2020). Double String Tandem Repeats. In I. L. Gortz, & O. Weimann (Eds.), 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020 Article 3 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 161). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.CPM.2020.3

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Amir, A, Butman, A, Landau, GM, Marcus, S & Sokol, D 2020, Double String Tandem Repeats. in IL Gortz & O Weimann (eds), 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020., 3, Leibniz International Proceedings in Informatics, LIPIcs, vol. 161, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020, Copenhagen, Denmark, 17/06/20. https://doi.org/10.4230/LIPIcs.CPM.2020.3

Double String Tandem Repeats. / Amir, Amihood; Butman, Ayelet; Landau, Gad M. et al.
31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020. ed. / Inge Li Gortz; Oren Weimann. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2020. 3 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 161).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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N2 - 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 UU0 such that U0 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. 2012 ACM Subject Classification Theory of computation ! Design and analysis of algorithms; Theory of computation ! Pattern matching.

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Double String Tandem Repeats

Abstract

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Bibliographical note

Funding

Keywords

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