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Abstract: Closest String is one of the core problems in the field of consensus word analysis with particular importance for computational biology. Given k strings of same length and a positive integer d, find a "closest string" s such that none of the given strings has Hamming distance greater than d from s. Closest String is NP-complete. We show how to solve Closest String in linear time for constant d (the exponential growth is O(d d )). We extend this result to the closely related problems d-Mismatch... (Update)
Context of citations to this paper: More
...than d to s. Closest String is NP complete. Here, we exploit two new techniques for solving Closest String (partially presented in [4]) and provide experimental evidence to show that they are practically useful for primer design and motif search (the experiments reported...
...1, 2, 3, 4 . CLOSEST STRING is NP complete. Here, we exploit two new techniques for solving CLOSEST STRING (partially presented in [4]) and provide experimental evidence to show that they are practically useful for primer design and motif search (the experiments reported here...
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BibTeX entry: (Update)
J. Gramm, R. Niedermeier, and P. Rossmanith. Exact solutions for Closest String and related problems. In Proc. of the 12th ISAAC, number 2223 in LNCS, pages 441--453, 2001. Springer. http://citeseer.ist.psu.edu/gramm01exact.html More
@article{ gramm01exact,
author = "Jens Gramm and Rolf Niedermeier and Peter Rossmanith",
title = "Exact Solutions for {CLOSEST {STRING}} and Related Problems",
journal = "Lecture Notes in Computer Science",
volume = "2223",
pages = "441+",
year = "2001",
url = "citeseer.ist.psu.edu/gramm01exact.html" }
Citations (may not include all citations):189 Parameterized Complexity - Downey, Fellows - 1999
49 Minkowski's convex body theorem and integer programming (context) - Kannan - 1987
46 Computational Molecular Biology: An Algorithmic Approach (context) - Pevzner - 2000
30 Faster exact solutions for hard problems: a parameterized po.. (context) - Alber, Gramm et al. - 2001
25 Integer programming with a xed number of variables (context) - Lenstra - 1983
17 Finding similar regions in many strings - Li, Ma et al. - 1999
14 Distinguishing string selection problems - Lanctot, Li et al. - 1999
13 Point lattices (context) - Lagarias - 1995
13 Theory of Computing Systems (context) - Frances, Litman et al. - 1997
10 A linear-time algorithm for the 1-mismatch problem (context) - Stojanovic, Berman et al. - 1997
4 Comparison of ve methods for nding conserved sequences in mu.. (context) - Stojanovic, Florea et al. - 1999
3 Practical non-polynomial time algorithms for designing unive.. (context) - Evans, Wareham - 2001
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