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Symposium on Combinatorial Pattern Matching

CPM 2014: Combinatorial Pattern Matching pp 100–109Cite as

Randomized and Parameterized Algorithms for the Closest String Problem

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8486))

Abstract

Given a set S = {s 1, s 2, …, s n } of strings of equal length L and an integer d, the closest string problem (CSP) requires the computation of a string s of length L such that d(s, s i ) ≤ d for each s i  ∈ S, where d(s, s i ) is the Hamming distance between s and s i . The problem is NP-hard and has been extensively studied in the context of approximation algorithms and parameterized algorithms. Parameterized algorithms provide the most practical solutions to its real-life applications in bioinformatics. In this paper we develop the first randomized parameterized algorithms for CSP. Not only are the randomized algorithms much simpler than their deterministic counterparts, their expected-time complexities are also significantly better than the previously best known (deterministic) algorithms.

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Author information

Authors and Affiliations

  1. Division of Information System Design, Tokyo Denki University, Hatoyama, Saitama, 350-0394, Japan

    Zhi-Zhong Chen

  2. School of Computer Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, Canada, N2L3G1

    Bin Ma

  3. Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR

    Lusheng Wang

Authors
  1. Zhi-Zhong Chen
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  2. Bin Ma
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  3. Lusheng Wang
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Editor information

Editors and Affiliations

  1. St. Petersburg Department of Steklov Institute of Mathematics, 27 Fontanka, 191023, St. Petersburg, Russia

    Alexander S. Kulikov

  2. National Research University Higher School of Economics, Bldg 3, Bolshoy Trekhsvyatitelskiy pereulok, 109028, Moscow, Russia

    Sergei O. Kuznetsov

  3. University of California at San Diego, 9500 Gilman Drive, EBU3b 4236, 92093-0404, La Jolla, CA, USA

    Pavel Pevzner

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Chen, ZZ., Ma, B., Wang, L. (2014). Randomized and Parameterized Algorithms for the Closest String Problem. In: Kulikov, A.S., Kuznetsov, S.O., Pevzner, P. (eds) Combinatorial Pattern Matching. CPM 2014. Lecture Notes in Computer Science, vol 8486. Springer, Cham. https://doi.org/10.1007/978-3-319-07566-2_11

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  • DOI: https://doi.org/10.1007/978-3-319-07566-2_11

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-07565-5

  • Online ISBN: 978-3-319-07566-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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