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Algorithms
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Algorithms
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Algorithms
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On String Matching with Mismatches

On string matching with mismatches
Authors: Nicolae, Marius; Rajasekaran, Sanguthevar;

On String Matching with Mismatches

Abstract

In this paper, we consider several variants of the pattern matching with mismatches problem. In particular, given a text \(T=t_1 t_2\cdots t_n\) and a pattern \(P=p_1p_2\cdots p_m\), we investigate the following problems: (1) pattern matching with mismatches: for every \(i, 1\leq i \leq n-m+1\) output, the distance between \(P\) and \(t_i t_{i+1}\cdots t_{i+m-1}\); and (2) pattern matching with \(k\) mismatches: output those positions \(i\) where the distance between \(P\) and \(t_i t_{i+1}\cdots t_{i+m-1}\) is less than a given threshold \(k\). The distance metric used is the Hamming distance. We present some novel algorithms and techniques for solving these problems. We offer deterministic, randomized and approximation algorithms. We consider variants of these problems where there could be wild cards in either the text or the pattern or both. We also present an experimental evaluation of these algorithms. The source code is available at http://www.engr.uconn.edu/\(\sim\)man09004/kmis.zip.

Keywords

Industrial engineering. Management engineering, Randomized algorithms, pattern matching with mismatches, QA75.5-76.95, T55.4-60.8, Algorithms on strings, Approximation algorithms, Electronic computers. Computer science, approximate counting of mismatches, k-mismatches problem, kmismatches problem

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
5
Average
Average
Average
gold