TY - GEN

T1 - From coding theory to efficient pattern matching

AU - Clifford, Raphaël

AU - Efremenko, Klim

AU - Porat, Ely

AU - Rothschild, Amir

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=70349090988&partnerID=8YFLogxK

U2 - 10.1137/1.9781611973068.85

DO - 10.1137/1.9781611973068.85

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AN - SCOPUS:70349090988

SN - 9780898716801

T3 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

SP - 778

EP - 784

BT - Proceedings of the 20th Annual ACM-SIAM Symposium on Discrete Algorithms

PB - Association for Computing Machinery (ACM)

T2 - 20th Annual ACM-SIAM Symposium on Discrete Algorithms

Y2 - 4 January 2009 through 6 January 2009

ER -