Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/15809
Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: The simplified partial digest problem: Approximation and a graph-theoretic model
Authors: Blazewicz, Jacek
Burke, Edmund
Kasprzak, Marta
Kovalev, Alexandr
Kovalyov, Mikhail Y
Contact Email: e.k.burke@stir.ac.uk
Keywords: Integer programming
Genome mapping
Combinatorial optimization
Heuristics
Approximation algorithms
Issue Date: Jan-2011
Publisher: Elsevier
Citation: Blazewicz J, Burke E, Kasprzak M, Kovalev A & Kovalyov MY (2011) The simplified partial digest problem: Approximation and a graph-theoretic model, European Journal of Operational Research, 208 (2), pp. 142-152.
Abstract: The goal of the simplified partial digest problem (SPDP) is motivated by the reconstruction of the linear structure of a DNA chain with respect to a given nucleotide pattern, based on the multiset of distances between the adjacent patterns (interpoint distances) and the multiset of distances between each pattern and the two unlabeled endpoints of the DNA chain (end distances). We consider optimization versions of the problem, called SPDP-Min and SPDP-Max. The aim of SPDP-Min (SPDP-Max) is to find a DNA linear structure with the same multiset of end distances and the minimum (maximum) number of incorrect (correct) interpoint distances. Results are presented on the worst-case efficiency of approximation algorithms for these problems. We suggest a graph-theoretic model for SPDP-Min and SPDP-Max, which can be used to reduce the search space for an optimal solution in either of these problems. We also present heuristic polynomial time algorithms based on this model. In computational experiments with randomly generated and real-life input data, our best algorithm delivered an optimal solution in 100% of the instances for a number of restriction sites not greater than 50.
Type: Journal Article
URI: http://hdl.handle.net/1893/15809
DOI Link: http://dx.doi.org/10.1016/j.ejor.2010.07.027
Rights: The publisher does not allow this work to be made publicly available in this Repository. Please use the Request a Copy feature at the foot of the Repository record to request a copy directly from the author. You can only request a copy if you wish to use this work for your own research or private study.
Affiliation: Poznan University of Technology
Deputy Principal's Office
Poznan University of Technology
Poznan University of Technology
National Academy of Sciences of Belarus

Files in This Item:
File Description SizeFormat 
The simplified partial digest problem.pdf832.45 kBAdobe PDFUnder Embargo until 31/12/2999     Request a copy

Note: If any of the files in this item are currently embargoed, you can request a copy directly from the author by clicking the padlock icon above. However, this facility is dependant on the depositor still being contactable at their original email address.

This item is protected by original copyright



Items in the Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

If you believe that any material held in STORRE infringes copyright, please contact library@stir.ac.uk providing details and we will remove the Work from public display in STORRE and investigate your claim.