Mismatch sampling

Raphaël Clifford; Klim Efremenko; Benny Porat; Ely Porat; Amir Rothschild

doi:10.1007/978-3-540-89097-3_11

Mismatch sampling

Raphaël Clifford
, Klim Efremenko
, Benny Porat
, Ely Porat
, Amir Rothschild

Department of Computer Science and Artificial Intelligence

University of Bristol
Bar-Ilan University
Weizmann Institute of Science
Tel Aviv University

Research output: Contribution to journal › Conference article › peer-review

Abstract

We consider the well known problem of pattern matching under the Hamming distance. Previous approaches have shown how to count the number of mismatches efficiently, especially when a bound is known for the maximum Hamming distance. Our interest is different in that we wish collect a random sample of mismatches of fixed size at each position in the text. Given a pattern p of length m and a text t of length n, we show how to sample with high probability c mismatches where possible from every alignment of p and t in O((c∈+∈logn) (n∈+∈mlogm)logm) time. Further, we guarantee that the mismatches are sampled uniformly and can therefore be seen as representative of the types of mismatches that occur.

Original language	English
Pages (from-to)	99-108
Number of pages	10
Journal	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5280 LNCS
DOIs	https://doi.org/10.1007/978-3-540-89097-3_11
State	Published - 2008
Event	15th International Symposium on String Processing and Information Retrieval, SPIRE 2008 - Melbourne. VIC, Australia Duration: 10 Nov 2008 → 12 Nov 2008

Bibliographical note

Funding Information:
This work was supported in part by the Binational Science Foundation (BSF) grant 2006334 and Israel Science Foundation (ISF) grant 1484/08 as well as the Engineering and Physical Sciences Research Council (EPSRC).

Funding

This work was supported in part by the Binational Science Foundation (BSF) grant 2006334 and Israel Science Foundation (ISF) grant 1484/08 as well as the Engineering and Physical Sciences Research Council (EPSRC).

Funders	Funder number
Engineering and Physical Sciences Research Council
United States-Israel Binational Science Foundation	2006334
Israel Science Foundation	1484/08

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10.1007/978-3-540-89097-3_11

Cite this

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title = "Mismatch sampling",

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AU - Porat, Benny

AU - Porat, Ely

AU - Rothschild, Amir

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Mismatch sampling

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