Double String Tandem Repeats

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

doi:10.1007/s00453-022-01016-9

Double String Tandem Repeats

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

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Journal	Algorithmica
DOIs	https://doi.org/10.1007/s00453-022-01016-9
State	Accepted/In press - 2022

Bibliographical note

Funding Information:
The authors A. Amir and G. M. Landau have been partially supported by Grant No. 2018141 from the United States-Israel Binational Science Foundation (BSF) and Israel Science Foundation Grant 1475-18. D. Sokol was also partially supported by BSF Grant No. 2018141. S. Marcus was partially supported by the Professional Staff Congress City University of New York Research Award 63164-00 51.

Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

2d corner sharing tandem
Double string
Scaled tandem repeat
Tandem repeat

ASJC Scopus subject areas

Computer Science (all)
Computer Science Applications
Applied Mathematics

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10.1007/s00453-022-01016-9

Cite this

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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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N1 - Funding Information: The authors A. Amir and G. M. Landau have been partially supported by Grant No. 2018141 from the United States-Israel Binational Science Foundation (BSF) and Israel Science Foundation Grant 1475-18. D. Sokol was also partially supported by BSF Grant No. 2018141. S. Marcus was partially supported by the Professional Staff Congress City University of New York Research Award 63164-00 51. Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

PY - 2022

Y1 - 2022

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 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.

AB - 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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Double String Tandem Repeats

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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