On the closest string and substring problems
نویسندگان
چکیده
منابع مشابه
More Efficient Algorithms for Closest String and Substring Problems
The closest string and substring problems find applications in PCR primer design, genetic probe design, motif finding, and antisense drug design. For their importance, the two problems have been extensively studied recently in computational biology. Unfortunately both problems are NP-complete. Researchers have developed both fixed-parameter algorithms and approximation algorithms for the two pr...
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Given a set S = {s1, s2, . . . , sn} of strings each of length m, and an integer L, we study the following two problems. k-Closest Substring problem: find k center strings c1, c2, . . . , ck of length L minimizing d such that for each sj ∈ S, there is a length-L substring tj (closest substring) of sj with min1≤i≤k d(ci, tj) ≤ d. We give a PTAS for this problem, for k = O(1). k-Consensus Pattern...
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We study two pattern matching problems that are motivated by applications in computational biology. In the Closest Substring problem k strings s1, . . ., sk are given, and the task is to find a string s of length L such that each string si has a consecutive substring of length L whose distance is at most d from s. We present two algorithms that aim to be efficient for small fixed values of d an...
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The closest substring problem, where a short string is sought that minimizes the number of mismatches between it and each of a given set of strings, is a minimization problem with a polynomial time approximation scheme [6]. In this paper, both this problem and its maximization complement, where instead the number of matches is maximized, are examined and bounds on their hardness of approximatio...
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Let S be a set of k strings over an alphabet Σ; each string has a length between ` and n. The Closest Substring Problem (CSSP) is to find a minimal integer d (and a corresponding string t of length `) such that each string s ∈ S has a substring of length ` with Hamming distance at most d to t. We say t is the closest substring to S. For ` = n, this problem is known as the Closest String Problem...
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ژورنال
عنوان ژورنال: Journal of the ACM
سال: 2002
ISSN: 0004-5411,1557-735X
DOI: 10.1145/506147.506150