From coding theory to efficient pattern matching

Raphaël Clifford, Klim Efremenko, Ely Porat, Amir Rothschild

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

28 Scopus citations

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.

Original languageEnglish
Title of host publicationProceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms
PublisherAssociation for Computing Machinery (ACM)
Pages778-784
Number of pages7
ISBN (Print)9780898716801
DOIs
StatePublished - 1 Jan 2009
Externally publishedYes
Event20th Annual ACM-SIAM Symposium on Discrete Algorithms - New York, NY, United States
Duration: 4 Jan 20096 Jan 2009

Publication series

NameProceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Conference

Conference20th Annual ACM-SIAM Symposium on Discrete Algorithms
Country/TerritoryUnited States
CityNew York, NY
Period4/01/096/01/09

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