On the complexity of the DNA simplified partial digest problem

Authors:
Jacek Blazewicz;Marta Kasprzak
Affiliations:
Institute of Computing Science, Poznan University of Technology, Poznan and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland;Institute of Computing Science, Poznan University of Technology, Poznan and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
Venue:
CATS '06 Proceedings of the 12th Computing: The Australasian Theroy Symposium - Volume 51
Year:
2006

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Abstract

The problem to be addressed is one of the genome mapping of DNA molecules. The new approach -- the Simplified Partial Digest Problem (SPDP), is analyzed. This approach is easy in laboratory implementation and robust with respect to measurement errors. In the paper, it is formulated in terms of a combinatorial search problem and proved to be strongly NP-hard for the general error-free case. For a subproblem of the SPDP, a simple O(n log n)-time algorithm is given, where n is a number of restriction sites.