Locating all maximal approximate runs in a string

Mika Amit, Maxime Crochemore, Gad M. Landau

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

Abstract

An exact run in a string, T, is a non-empty substring of T that can be divided into adjacent non-overlapping identical substrings. Finding exact runs in strings is an important problem and therefore a well studied one in the strings community. For a given string T of length n, finding all maximal exact runs in the string can be done in O(n logn) time or O(n) time on integer alphabets. In this paper, we investigate the maximal approximate runs problem: for a given string T and a number k, find every non-empty substring T′ of T such that changing at most k letters in T′ transforms it into a maximal exact run in T. We present an O(nk2 log k log n/k) algorithm.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings
Pages13-27
Number of pages15
DOIs
StatePublished - 2013
Event24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013 - Bad Herrenalb, Germany
Duration: 17 Jun 201319 Jun 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7922 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013
Country/TerritoryGermany
CityBad Herrenalb
Period17/06/1319/06/13

Keywords

  • algorithms on strings
  • pattern matching
  • repetitions
  • runs
  • tandem repeats

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

Fingerprint

Dive into the research topics of 'Locating all maximal approximate runs in a string'. Together they form a unique fingerprint.

Cite this