Finding the position of the k-mismatch and approximate tandem repeats

Haim Kaplan, Ely Porat, Nira Shafrir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Given a pattern P, a text T, and an integer k, we want to find for every position j of T, the index of the k-mismatch of P with the suffix of T starting at position j. We give an algorithm that finds the exact index for each j, and algorithms that approximate it. We use these algorithms to get an efficient solution for an approximate version of the tandem repeats problem with k-mismatches.

Original languageEnglish
Title of host publicationBiomedical Simulation - Third International Symposium, ISBMS 2006, Proceedings
PublisherSpringer Verlag
Pages90-101
Number of pages12
ISBN (Print)354035753X, 9783540357537
DOIs
StatePublished - 2006
Event10th Scandinavian Workshop on Algorithm Theory, SWAT 2006 - Riga, Latvia
Duration: 6 Jul 20068 Jul 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4059 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference10th Scandinavian Workshop on Algorithm Theory, SWAT 2006
Country/TerritoryLatvia
CityRiga
Period6/07/068/07/06

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