Algorithmic Topics in Bioinformatics : The Partial Digest Problem ( Paper for CSE 202
نویسندگان
چکیده
منابع مشابه
Modeling of Partial Digest Problem as a Network flows problem
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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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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A fundamental problem in computational biology is the construction of physical maps of chromosomes from the hybridization experiments between unique probes and clones of chromosome fragments. Double and partial digest problems are two intractable problems used to construct physical maps of DNA molecules in bioinformatics. Several approaches, including exponential algorithms and heuristic algori...
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MOTIVATION A formulation of a new problem of the restriction map construction based on a simplified digestion experiment and a development of an algorithm for solving both ideal and noisy data cases of the introduced problem. RESULTS A simplified partial digest problem and a branch and cut algorithm for finding the solution of the problem.
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A computer algorithm for restriction-site mapping consists of a generator of partial maps and a consistency checker. This paper examines consistency checking and argues that a method based on separation theory extracts the maximum amount of information from fragment lengths in digest data. It results in the minimum number of false maps being generated.
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