Pattern matching with don't cares and few errors

Raphaël Clifford, Klim Efremenko, Ely Porat, Amir Rothschild

Research output: Contribution to journalConference articlepeer-review


We present solutions 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 Θ (n(k + log m log k) log n) time randomised algorithm which finds the correct answer with high probability. We then present a new deterministic Θ `nk2 log2 m´ time solution that uses tools originally developed for group testing. Taking our derandomisation approach further we develop an approach based on k-selectors that runs in Θ (nk polylogm) time. Further, in each case the location of the mismatches at each alignment is also given at no extra cost.

Original languageEnglish
JournalDagstuhl Seminar Proceedings
StatePublished - 2009
EventSearch Methodologies 2009 - Wadern, Germany
Duration: 5 Jul 200910 Jul 2009

Bibliographical note

Publisher Copyright:
© 2009 Dagstuhl Seminar Proceedings. All rights reserved.


∗Research supported in part by the Binational Science Foundation (BSF)

FundersFunder number
British Skin Foundation
United States-Israel Binational Science Foundation


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