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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Veröffentlicht in:Algorithmica Jg. 74; H. 1; S. 466 - 484
Hauptverfasser: Chen, Zhi-Zhong, Ma, Bin, Wang, Lusheng
Format: Journal Article
Sprache:Englisch
Veröffentlicht: New York Springer US 01.01.2016
Schlagworte:
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
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Zusammenfassung: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