Pattern matching with don't cares and few errors

Clifford, Raphael; Efremo, Klim; Porat, Ely; Rotschild, Amir

doi:10.4230/DagSemProc.09281.5

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Pattern matching with don't cares and few errors

Authors Raphael Clifford, Klim Efremo, Ely Porat, Amir Rotschild

Part of: Volume: Dagstuhl Seminar Proceedings, Volume 9281
Part of: Series: Dagstuhl Seminar Proceedings (DagSemProc)
License: Creative Commons Attribution 4.0 International license
Publication Date: 2009-11-10

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DagSemProc.09281.5.pdf

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Document Identifiers

DOI: 10.4230/DagSemProc.09281.5
URN: urn:nbn:de:0030-drops-22442

Subject Classification

Keywords

Prime Numbers
Group Testing
Streaming
Pattern Matching

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Abstract

We present solutions 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 and a bound k, our algorithms find all the places
that the pattern matches the text with at most k mismatches. We first
give an \Theta(n(k + logmlog k) log n) time randomised algorithm which finds
the correct answer with high probability. We then present a new deter-
ministic \Theta(nk^2 log^m)time solution that uses tools originally developed
for group testing. Taking our derandomisation approach further we de-
velop an approach based on k-selectors that runs in \Theta(nk polylogm) time.
Further, in each case the location of the mismatches at each alignment is
also given at no extra cost.

Cite As Get BibTex

Raphael Clifford, Klim Efremo, Ely Porat, and Amir Rotschild. Pattern matching with don't cares and few errors. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009) https://doi.org/10.4230/DagSemProc.09281.5

Author Details

Raphael Clifford

Klim Efremo

Ely Porat

Amir Rotschild

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