Randomized Fixed-Parameter Algorithms for the Closest String Problem

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

5 Scopus Citations
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Detail(s)

Original languageEnglish
Pages (from-to)466-484
Journal / PublicationAlgorithmica
Volume74
Issue number1
Online published28 Oct 2014
Publication statusPublished - Jan 2016

Abstract

Given a set = {s1s2,…, sn} of strings of equal length L and an integer d, the closest string problem (CSP) requires the computation of a string s of length such that (ssi) ≤ d for each si ∈ S, where (ssi) is the Hamming distance between s and si. The problem is NP-hard and has been extensively studied in the context of approximation algorithms and fixed-parameter algorithms. Fixed-parameter algorithms provide the most practical solutions to its real-life applications in bioinformatics. In this paper we develop the first randomized fixed-parameter algorithms for CSP. Not only are the randomized algorithms much simpler than their deterministic counterparts, their time complexities are also significantly better than the previously best known (deterministic) algorithms.

Research Area(s)

  • Computational biology, Fixed-parameter algorithms, Randomized algorithms, The closest string problem

Citation Format(s)

Randomized Fixed-Parameter Algorithms for the Closest String Problem. / Chen, Zhi-Zhong; Ma, Bin; Wang, Lusheng.
In: Algorithmica, Vol. 74, No. 1, 01.2016, p. 466-484.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review