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...

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...

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...

The Partial Digest problem asks for the coordinates of m points on a line such that the pairwise distances of the points form a given multiset of (m 2 ) distances. Partial Digest is a well-studied problem with important applications in physical mapping of DNA molecules. Its computational complexity status is open. Input data for Partial Digest from real-life experiments are always prone to erro...

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...

The problem to find the coordinates of n points on a line such that the pairwise distances of the points form a given multi-set of n 2 distances is known as Partial Digest problem, which occurs for instance in DNA physical mapping and de novo sequencing of proteins. Although Partial Digest was – as a combinatorial problem – already proposed in the 1930’s, its computational complexity is still u...

The Partial Digest problem { well-known for its applications in computational biology and for the intriguingly open status of its computational complexity { asks for the coordinates of n points on a line such that the pairwise distances of the points form a given multi-set of ? n 2 distances. In an eeort to model real-life data, we study the computational complexity of a minimization version of...