Combinatorial optimization in DNA mapping - A computational thread of the simplified partial digest problem
RAIRO - Operations Research - Recherche Opérationnelle, Volume 39 (2005) no. 4, p. 227-241

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($n\phantom{\rule{0.166667em}{0ex}}\mathrm{log}\phantom{\rule{0.166667em}{0ex}}n$)-time algorithm is given, where $n$ is a number of restriction sites.

DOI : https://doi.org/10.1051/ro:2006007
Keywords: combinatorial optimization, DNA restriction mapping, partial digest, computational complexity
@article{RO_2005__39_4_227_0,
author = {Blazewicz, Jacek and Kasprzak, Marta},
title = {Combinatorial optimization in DNA mapping - A computational thread of the simplified partial digest problem},
journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
publisher = {EDP-Sciences},
volume = {39},
number = {4},
year = {2005},
pages = {227-241},
doi = {10.1051/ro:2006007},
zbl = {pre05233849},
language = {en},
url = {http://www.numdam.org/item/RO_2005__39_4_227_0}
}

Blazewicz, Jacek; Kasprzak, Marta. Combinatorial optimization in DNA mapping - A computational thread of the simplified partial digest problem. RAIRO - Operations Research - Recherche Opérationnelle, Volume 39 (2005) no. 4, pp. 227-241. doi : 10.1051/ro:2006007. http://www.numdam.org/item/RO_2005__39_4_227_0/

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