An algorithm for approximate tandem repeats

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
G M LandauDina Sokol

Abstract

A perfect single tandem repeat is defined as a nonempty string that can be divided into two identical substrings, e.g., abcabc. An approximate single tandem repeat is one in which the substrings are similar, but not identical, e.g., abcdaacd. 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 = umacro û, for which the Hamming distance of umacro and û is at most k, in O(nk log (n/k)) time, or all those for which the edit distance of umacro and û is at most k, in O(nk log k log (n/k)) time. This paper concentrates on a more general type of repeat called multiple tandem repeats. A multiple tandem repeat in a sequence S is a (periodic) substring r of S of the form r = u(a)u', where u is a prefix of r and u' is a prefix of u. An approximate multiple tandem repeat is a multiple repeat with errors; the repeated subsequences are similar but not identical. We precisely define approximate multiple repeats, and present an algorithm that finds all repeats that concur with our definition. The time complexity of the algorithm, when searching for repeats wi...Continue Reading

References

Jan 1, 1990·Methods in Enzymology·R F Doolittle
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Nov 11, 1994·Nucleic Acids Research·G Benson, M S Waterman
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·G Benson
May 16, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·G Benson, X Su
Dec 24, 1998·Nucleic Acids Research·G Benson

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Citations

Oct 6, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ydo WexlerDan Geiger
Jun 10, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Vera P TurutinaEugene V Korotkov
Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nevzat Onur Domaniç, Franco P Preparata
Jul 16, 2008·Briefings in Bioinformatics·Angelika Merkel, Neil Gemmell
Jan 24, 2007·Bioinformatics·Dina SokolJustin Tojeira
Aug 13, 2009·Bioinformatics·Julien Jorda, Andrey V Kajava
Jun 10, 2010·Bioinformatics·Marco PellegriniAlessio Vecchio
Jul 14, 2010·Database : the Journal of Biological Databases and Curation·Dina Sokol, Firat Atagun
Jun 26, 2003·Nucleic Acids Research·Roman KolpakovGregory Kucherov
Nov 29, 2011·Nucleic Acids Research·Atheer A MatroudC P Tuffley
Feb 7, 2006·Biochemistry. Biokhimii︠a︡·V P TurutinaE V Korotkov
Aug 24, 2007·EURASIP Journal on Bioinformatics & Systems Biology·Ravi GuptaKuldip Singh
Apr 20, 2007·BMC Bioinformatics·Sébastien LeclercqPhilippe Jarne
Jun 3, 2010·BMC Genomics·Eric C Rouchka
Jun 24, 2011·Evolutionary Bioinformatics Online·Valerio Freschi, Alessandro Bogliolo
Sep 24, 2004·IEEE Transactions on Nanobioscience·Chun-Hsi Huang, Sanguthevar Rajasekaran
Sep 19, 2006·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Andrew ShelenkovEugene Korotkov
Dec 23, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ana M JelovicMilos V Beljanski
Apr 21, 2012·Evolutionary Bioinformatics Online·Valerio Freschi, Alessandro Bogliolo

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