Combinatorial optimization in DNA mapping — a computational thread of the Simplified Partial Digest Problem
نویسندگان
چکیده
منابع مشابه
Combinatorial optimization in DNA mapping - a computational thread of the Simplified Partial Digest Problem
In the paper, the problem of the genome mapping of DNA molecules, is presented. In particular, the new approach — the Simplified Partial Digest Problem (SPDP), is analyzed. This approach, although easy in laboratory implementation and robust with respect to measurement errors, when formulated in terms of a combinatorial search problem, is proved to be strongly NP-hard for the general errorfree ...
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The pupose of this paper is modeling of Partial Digest Problem (PDP) as a mathematical programming problem. In this paper we present a new viewpoint of PDP. We formulate the PDP as a continuous optimization problem and develope a method to solve this problem. Finally we constract a linear programming model for the problem with an additional constraint. This later model can be solved by the simp...
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Restriction Site Mapping is one of the interesting tasks in Computational Biology. A DNA strand can be thought of as a string on the letters A, T, C, and G. When a particular restriction enzyme is added to a DNA solution, the DNA is cut at particular restriction sites. The goal of the restriction site mapping is to determine the location of every site for a given enzyme. In partial digest metho...
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Introduction We study the problem of genome mapping using restriction site analysis. In restriction site analysis, an enzyme cuts a target DNA strand into DNA fragments, and these DNA fragments are used to reconstruct the restriction site locations of the enzyme. Two common approaches are the Double Digest Problem and the Partial Digest Problem. The Double Digest Problem is known to be NP-Compl...
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the pupose of this paper is modeling of partial digest problem (pdp) as a mathematical programming problem. in this paper we present a new viewpoint of pdp. we formulate the pdp as a continuous optimization problem and develope a method to solve this problem. finally we constract a linear programming model for the problem with an additional constraint. this later model can be solved by the simp...
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ژورنال
عنوان ژورنال: RAIRO - Operations Research
سال: 2005
ISSN: 0399-0559,1290-3868
DOI: 10.1051/ro:2006007