We study the Simplified Partial Digest Problem (SPDP), which is a mathematical model for a new simplified partial digest method of genome mapping. This method is easy for laboratory implementation and robust with respect to the experimental errors. SPDP is NP-hard in the strong sense. We present an Oðn2Þ time enumerative algorithm (ENUM) and an OðnÞ time dynamic programming algorithm for the er...

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

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.

We state in previous paper [3] that the chords’ problem can be solved in polynomial time. This result is however ambiguous and some people have been abused because the encoding of the data has not been given. The correctness of the result requires to specify the encoding of the data that we have used and to highlight the difference with the usual encoding implicitly considered in Partial Digest...

We revisit the double digest problem, which occurs in sequencing of large DNA strings and consists of reconstructing the relative positions of cut sites from two different enzymes: we rst show that double digest is strongly NP-complete, improving previous results that only showed weak NP-completeness. Even the (experimentally more meaningful) variation in which we disallow coincident cut sites ...

We present a new, practical algorithm to resolve the experimental data in restriction site analysis, which is a common technique for mapping DNA. Speciically, we assert that multiple digestions with a single restriction enzyme can provide suucient information to identify the positions of the restriction sites with high probability. The motivation for the new approach comes from combinatorial re...