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Combinatorial optimization in DNA mapping — a computational threadof the Simplified Partial Digest Problem

Published online by Cambridge University Press:  08 April 2006

Jacek Blazewicz  and
Marta Kasprzak
Jacek Blazewicz
Affiliation:
Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60–965 Poznan, Poland; jblazewicz@cs.put.poznan.pl Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; marta@cs.put.poznan.pl
Marta Kasprzak
Affiliation:
Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60–965 Poznan, Poland; jblazewicz@cs.put.poznan.pl Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; marta@cs.put.poznan.pl
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Abstract

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 error-free case. For a subproblem of the SPDP, a simple O(nlogn)-time algorithm is given, where n is a number of restriction sites.

Keywords

Combinatorial optimizationDNA restriction mappingpartial digestcomputational complexity.
Type
Research Article
Information
RAIRO - Operations Research , Volume 39 , Issue 4 , October 2005 , pp. 227 - 241
Copyright
© EDP Sciences, 2006

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