An algorithm for approximate tandem repeats

Gad M. Landau; Jeanette P. Schmidt

doi:10.1007/bfb0029801

An algorithm for approximate tandem repeats

Gad M. Landau, Jeanette P. Schmidt

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

Abstract

A perfect tandem repeat within a string S is a substring r = r₁,… r_2l of S, for which r₁… r₁ = r_l+1 … r_2l. An approximate tandem repeat is a substring r =r₁,…, r_l¹,… rl, for which r₁,…, r_1^l and r_l¹+1,… r_l are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = ūȗ, for which the Hamming distance of u and ȗ is at most k in O(nklog(n/k)) time, or all those for which the edit distance of ū and ȗ is at most k, in O(nk log k log n) time.

Original language	English
Title of host publication	Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings
Editors	Alberto Apostolico, Alberto Apostolico, Maxime Crochemore , Zvi Galil, Zvi Galil, Udi Manber
Publisher	Springer Verlag
Pages	120-133
Number of pages	14
ISBN (Print)	9783540567646
DOIs	https://doi.org/10.1007/bfb0029801
State	Published - 1993
Externally published	Yes
Event	Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017 - Warsaw, Poland Duration: 11 Sep 2017 → 15 Sep 2017

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	684 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017
Country/Territory	Poland
City	Warsaw
Period	11/09/17 → 15/09/17

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 1993.

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/bfb0029801

Cite this

Landau, G. M., & Schmidt, J. P. (1993). An algorithm for approximate tandem repeats. In A. Apostolico, A. Apostolico, M. Crochemore , Z. Galil, Z. Galil, & U. Manber (Eds.), Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings (pp. 120-133). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 684 LNCS). Springer Verlag. https://doi.org/10.1007/bfb0029801

Landau, Gad M. ; Schmidt, Jeanette P. / An algorithm for approximate tandem repeats. Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. editor / Alberto Apostolico ; Alberto Apostolico ; Maxime Crochemore ; Zvi Galil ; Zvi Galil ; Udi Manber. Springer Verlag, 1993. pp. 120-133 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{972833f7abd840caad693429ed138fba,

title = "An algorithm for approximate tandem repeats",

abstract = "A perfect tandem repeat within a string S is a substring r = r1,… r2l of S, for which r1… r1 = rl+1 … r2l. An approximate tandem repeat is a substring r =r1,…, rl1 ,… rl, for which r1,…, r1l and rl1+1,… rl are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = ūȗ, for which the Hamming distance of u and ȗ is at most k in O(nklog(n/k)) time, or all those for which the edit distance of ū and ȗ is at most k, in O(nk log k log n) time.",

author = "Landau, {Gad M.} and Schmidt, {Jeanette P.}",

note = "Publisher Copyright: {\textcopyright} Springer-Verlag Berlin Heidelberg 1993.; Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017 ; Conference date: 11-09-2017 Through 15-09-2017",

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doi = "10.1007/bfb0029801",

language = "English",

isbn = "9783540567646",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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Landau, GM & Schmidt, JP 1993, An algorithm for approximate tandem repeats. in A Apostolico, A Apostolico, M Crochemore , Z Galil, Z Galil & U Manber (eds), Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 684 LNCS, Springer Verlag, pp. 120-133, Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017, Warsaw, Poland, 11/09/17. https://doi.org/10.1007/bfb0029801

An algorithm for approximate tandem repeats. / Landau, Gad M.; Schmidt, Jeanette P.
Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. ed. / Alberto Apostolico; Alberto Apostolico; Maxime Crochemore ; Zvi Galil; Zvi Galil; Udi Manber. Springer Verlag, 1993. p. 120-133 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 684 LNCS).

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

TY - GEN

T1 - An algorithm for approximate tandem repeats

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AU - Schmidt, Jeanette P.

N1 - Publisher Copyright: © Springer-Verlag Berlin Heidelberg 1993.

PY - 1993

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N2 - A perfect tandem repeat within a string S is a substring r = r1,… r2l of S, for which r1… r1 = rl+1 … r2l. An approximate tandem repeat is a substring r =r1,…, rl1 ,… rl, for which r1,…, r1l and rl1+1,… rl are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = ūȗ, for which the Hamming distance of u and ȗ is at most k in O(nklog(n/k)) time, or all those for which the edit distance of ū and ȗ is at most k, in O(nk log k log n) time.

AB - A perfect tandem repeat within a string S is a substring r = r1,… r2l of S, for which r1… r1 = rl+1 … r2l. An approximate tandem repeat is a substring r =r1,…, rl1 ,… rl, for which r1,…, r1l and rl1+1,… rl are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = ūȗ, for which the Hamming distance of u and ȗ is at most k in O(nklog(n/k)) time, or all those for which the edit distance of ū and ȗ is at most k, in O(nk log k log n) time.

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BT - Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings

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A2 - Manber, Udi

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Y2 - 11 September 2017 through 15 September 2017

ER -

Landau GM, Schmidt JP. An algorithm for approximate tandem repeats. In Apostolico A, Apostolico A, Crochemore M, Galil Z, Galil Z, Manber U, editors, Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings. Springer Verlag. 1993. p. 120-133. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/bfb0029801

An algorithm for approximate tandem repeats

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