A filtering algorithm for k-mismatch with don't cares

Raphaël Clifford; Ely Porat

doi:10.1007/978-3-540-75530-2_12

A filtering algorithm for k-mismatch with don't cares

Raphaël Clifford, Ely Porat

Department of Computer Science

University of Bristol

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

11 Scopus citations

Abstract

We present a filtering based algorithm 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 in either p or t and a bound k, our algorithm finds all the places that the pattern matches the text with at most k mismatches. The algorithm is deterministic and runs in O(nm^1/3k^1/3 log^2/3 m) time. The location of the mismatches at each alignment is also given at no extra cost.

Original language	English
Title of host publication	String Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings
Publisher	Springer Verlag
Pages	130-136
Number of pages	7
ISBN (Print)	9783540755296
DOIs	https://doi.org/10.1007/978-3-540-75530-2_12
State	Published - 2007
Event	14th International Symposium on String Processing and Information Retrieval, SPIRE 2007 - Santiago, Chile Duration: 29 Oct 2007 → 31 Oct 2007

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4726 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	14th International Symposium on String Processing and Information Retrieval, SPIRE 2007
Country/Territory	Chile
City	Santiago
Period	29/10/07 → 31/10/07

Access to Document

10.1007/978-3-540-75530-2_12

Cite this

Clifford, R., & Porat, E. (2007). A filtering algorithm for k-mismatch with don't cares. In String Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings (pp. 130-136). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4726 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-540-75530-2_12

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title = "A filtering algorithm for k-mismatch with don't cares",

abstract = "We present a filtering based algorithm 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 in either p or t and a bound k, our algorithm finds all the places that the pattern matches the text with at most k mismatches. The algorithm is deterministic and runs in O(nm1/3k1/3 log2/3 m) time. The location of the mismatches at each alignment is also given at no extra cost.",

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Clifford, R & Porat, E 2007, A filtering algorithm for k-mismatch with don't cares. in String Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4726 LNCS, Springer Verlag, pp. 130-136, 14th International Symposium on String Processing and Information Retrieval, SPIRE 2007, Santiago, Chile, 29/10/07. https://doi.org/10.1007/978-3-540-75530-2_12

A filtering algorithm for k-mismatch with don't cares. / Clifford, Raphaël; Porat, Ely.
String Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings. Springer Verlag, 2007. p. 130-136 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4726 LNCS).

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

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Clifford R, Porat E. A filtering algorithm for k-mismatch with don't cares. In String Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings. Springer Verlag. 2007. p. 130-136. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-75530-2_12

A filtering algorithm for k-mismatch with don't cares

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