Randomized Fixed-Parameter Algorithms for the Closest String Problem

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...

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Bibliographic Details
Published in:	Algorithmica Vol. 74; no. 1; pp. 466 - 484
Main Authors:	Chen, Zhi-Zhong, Ma, Bin, Wang, Lusheng
Format:	Journal Article
Language:	English
Published:	New York Springer US 01.01.2016
Subjects:	Algorithm Analysis and Problem Complexity Algorithms Computer Science Computer Systems Organization and Communication Networks Data Structures and Information Theory Mathematics of Computing Theory of Computation Randomized algorithms Fixed-parameter algorithms The closest string problem Computational biology
ISSN:	0178-4617, 1432-0541
Online Access:	Get full text
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Summary:	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 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.
ISSN:	0178-4617 1432-0541
DOI:	10.1007/s00453-014-9952-y