A Three-String Approach to the Closest String Problem View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2010

AUTHORS

Zhi-Zhong Chen , Bin Ma , Lusheng Wang

ABSTRACT

Given a set of n strings of length L and a radius d, the closest string problem asks for a new string tsol that is within a Hamming distance of d to each of the given strings. It is known that the problem is NP-hard and its optimization version admits a polynomial time approximation scheme (PTAS). Parameterized algorithms have been then developed to solve the problem when d is small. In this paper, with a new approach (called the 3-string approach), we first design a parameterized algorithm for binary strings that runs in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$O\left(nL + nd^3 6.731^d\right)$\end{document} time, while the previous best runs in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$O\left(nL + nd 8^d\right)$\end{document} time. We then extend the algorithm to arbitrary alphabet sizes, obtaining an algorithm that runs in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$ O \left( nL + nd 1.612^d \left( \alpha^2 +1 - 2 \alpha^{-1} + \alpha^{-2} \right) ^{3d}\right) $\end{document} time, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\alpha = \sqrt[3]{\mathstrut \sqrt{|\Sigma|-1}+1 }$\end{document}. This new time bound is better than the previous best for small alphabets, including the very important case where |Σ| = 4 (i.e., the case of DNA strings). More... »

PAGES

449-458

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-642-14031-0_48

DOI

http://dx.doi.org/10.1007/978-3-642-14031-0_48

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1016511591


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