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Author Li, Ming ♦ Ma, Bin ♦ Wang, Lusheng
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2002
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Closest string and substring ♦ Computer applications ♦ Polynomial-time approximation scheme
Abstract The problem of finding a center string that is "close" to everygiven string arises in computational molecular biology and codingtheory. This problem has two versions: the Closest String problemand the Closest Substring problem. Given a set of strings $\textit{S}=$ ${s_{1},$ $s_{2},$ $...,s_{n}},$ each of length $\textit{m},$ the Closest Stringproblem is to find the smallest $\textit{d}$ and a string s of $length\textit{m}$ which is within Hamming distance d to $eachs_{i}$ ε $\textit{S}.$ This problem comes fromcoding theory when we are looking for a code not too far away froma given set of codes. Closest Substring problem, with an additionalinput integer $\textit{L},$ asks for the smallest d and a $string\textit{s},$ of length $\textit{L},$ which is within Hamming distance daway from a substring, of length $\textit{L},$ of each si. This problemis much more elusive than the Closest String problem. The ClosestSubstring problem is formulated from applications in findingconserved regions, identifying genetic drug targets and generatinggenetic probes in molecular biology. Whether there are efficientapproximation algorithms for both problems are major open questionsin this area. We present two polynomial-time approximationalgorithms with approximation ratio 1 + ε for any smallε to settle both questions.
ISSN 00045411
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2002-03-01
Publisher Place New York
e-ISSN 1557735X
Journal Journal of the ACM (JACM)
Volume Number 49
Issue Number 2
Page Count 15
Starting Page 157
Ending Page 171


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Source: ACM Digital Library