TY - JOUR
T1 - Randomized Fixed-Parameter Algorithms for the Closest String Problem
AU - Chen, Zhi-Zhong
AU - Ma, Bin
AU - Wang, Lusheng
PY - 2016/1
Y1 - 2016/1
N2 - Given a set S = {s1, s2,…, 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 L such that d (s, si) ≤ d for each si ∈ S, where d (s, si) 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.
AB - Given a set S = {s1, s2,…, 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 L such that d (s, si) ≤ d for each si ∈ S, where d (s, si) 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.
KW - Computational biology
KW - Fixed-parameter algorithms
KW - Randomized algorithms
KW - The closest string problem
UR - http://www.scopus.com/inward/record.url?scp=84953357368&partnerID=8YFLogxK
UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-84953357368&origin=recordpage
U2 - 10.1007/s00453-014-9952-y
DO - 10.1007/s00453-014-9952-y
M3 - RGC 21 - Publication in refereed journal
VL - 74
SP - 466
EP - 484
JO - Algorithmica
JF - Algorithmica
SN - 0178-4617
IS - 1
ER -