Next Article in Journal
Dynamics and Fractal Dimension of Steffensen-Type Methods
Next Article in Special Issue
Modified Classical Graph Algorithms for the DNA Fragment Assembly Problem
Previous Article in Journal
An Optimization Clustering Algorithm Based on Texture Feature Fusion for Color Image Segmentation
Article Menu

Export Article

Open AccessArticle
Algorithms 2015, 8(2), 248-270; doi:10.3390/a8020248

On String Matching with Mismatches

Department of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way Unit 4155, Storrs, CT 06269, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Giuseppe Lancia
Received: 3 April 2015 / Accepted: 19 May 2015 / Published: 26 May 2015
(This article belongs to the Special Issue Algorithmic Themes in Bioinformatics)
View Full-Text   |   Download PDF [405 KB, uploaded 26 May 2015]   |  

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. View Full-Text
Keywords: pattern matching with mismatches; kmismatches problem; approximate counting of mismatches pattern matching with mismatches; kmismatches problem; approximate counting of mismatches
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Nicolae, M.; Rajasekaran, S. On String Matching with Mismatches. Algorithms 2015, 8, 248-270.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Algorithms EISSN 1999-4893 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top