From coding theory to efficient pattern matching

Raphaël Clifford; Klim Efremenko; Ely Porat; Amir Rothschild

doi:10.1137/1.9781611973068.85

From coding theory to efficient pattern matching

Raphaël Clifford, Klim Efremenko, Ely Porat, Amir Rothschild

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

31 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 language	English
Title of host publication	Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms
Publisher	Association for Computing Machinery (ACM)
Pages	778-784
Number of pages	7
ISBN (Print)	9780898716801
DOIs	https://doi.org/10.1137/1.9781611973068.85
State	Published - 2009
Event	20th Annual ACM-SIAM Symposium on Discrete Algorithms - New York, NY, United States Duration: 4 Jan 2009 → 6 Jan 2009

Publication series

Name	Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Conference

Conference	20th Annual ACM-SIAM Symposium on Discrete Algorithms
Country/Territory	United States
City	New York, NY
Period	4/01/09 → 6/01/09

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10.1137/1.9781611973068.85

Cite this

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title = "From coding theory to efficient pattern matching",

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 {\~O}(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.",

author = "Rapha{\"e}l Clifford and Klim Efremenko and Ely Porat and Amir Rothschild",

year = "2009",

doi = "10.1137/1.9781611973068.85",

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series = "Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms",

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pages = "778--784",

booktitle = "Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms",

address = "ארצות הברית",

note = "20th Annual ACM-SIAM Symposium on Discrete Algorithms ; Conference date: 04-01-2009 Through 06-01-2009",

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Clifford, R, Efremenko, K, Porat, E & Rothschild, A 2009, From coding theory to efficient pattern matching. in Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Association for Computing Machinery (ACM), pp. 778-784, 20th Annual ACM-SIAM Symposium on Discrete Algorithms, New York, NY, United States, 4/01/09. https://doi.org/10.1137/1.9781611973068.85

From coding theory to efficient pattern matching. / Clifford, Raphaël; Efremenko, Klim; Porat, Ely et al.
Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms. Association for Computing Machinery (ACM), 2009. p. 778-784 (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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From coding theory to efficient pattern matching

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