From coding theory to efficient pattern matching

R Clifford, Efremenko Klim, Porat Ely, Rothschild Amir

Research output: Chapter in Book/Report/Conference proceedingConference Contribution (Conference Proceeding)

26 Citations (Scopus)

Abstract

We consider the classic problem of pattern matching with few mismatches in the presence of promiscuously matching wildcard symbols. Given a text t of length n and a pattern p of length m with optional wildcard symbols and a bound k, our algorithm finds all the alignments for which the pattern matches the text with Hamming distance at most k and also returns the location and identity of each mismatch. The algorithm we present is deterministic and runs in Õ(kn) time, matching the best known randomised time complexity to within logarithmic factors. The solutions we develop borrow from the tool set of algebraic coding theory and provide a new framework in which to tackle approximate pattern matching problems.
Translated title of the contributionFrom coding theory to efficient pattern matching
Original languageEnglish
Title of host publicationSODA '09 Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms
PublisherAssociation for Computing Machinery (ACM)
Pages778 - 784
Number of pages7
ISBN (Print)9781618394019
Publication statusPublished - 2009

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