K-mismatch with don't cares

Raphaël Clifford, Klim Efremenko, Ely Porat, Amir Rothschild

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

27 Scopus citations

Abstract

We give the first non-trivial algorithms for the k-mismatch pattern matching problem with don't cares. Given a text t of length n and a pattern p of length m with don't care symbols and a bound k, our algorithms find all the places that the pattern matches the text with at most k mismatches. We first give an O(n(k + log n log log n) log m) time randomised solution which finds the correct answer with high probability. We then present a new deterministic O(nk2 log3 m) time solution that uses tools developed for group testing and finally an approach based on k-selectors that runs in O(nk polylog m) time but requires O(poly m) time preprocessing. In each case, the location of the mismatches at each alignment is also given at no extra cost.

Original languageEnglish
Title of host publicationAlgorithms - ESA 2007 - 15th Annual European Symposium, Proceedings
PublisherSpringer Verlag
Pages151-162
Number of pages12
ISBN (Print)9783540755197
DOIs
StatePublished - 1 Jan 2007
Externally publishedYes
Event15th Annual European Symposium on Algorithms, ESA 2007 - Eilat, Israel
Duration: 8 Oct 200710 Oct 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4698 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference15th Annual European Symposium on Algorithms, ESA 2007
Country/TerritoryIsrael
CityEilat
Period8/10/0710/10/07

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