Combinatorial Optimization Algorithms

  • Elisa Pappalardo
  • Beyza Ahlatcioglu Ozkok
  • Panos M. Pardalos
Reference work entry


Identification of targets, generally virus or bacteria, in a biological sample is a relevant problem in medicine. Biologists can use hybridization experiments to determine whether a specific DNA fragment, that represents the virus, is present in a DNA solution. A probe is a segment of DNA or RNA, labeled with a radioactive isotope, dye, or enzyme, used to find a specific target sequence on a DNA molecule by hybridization. Selecting unique probes through hybridization experiments is a difficult task, especially when targets have a high degree of similarity, for instance, in case of closely related viruses.The nonunique probe selection problem is a challenging problem from a biological and computational point of view; a plethora of methods have been proposed in literature ranging from evolutionary algorithms to mathematical programming approaches.In this study, we conducted a survey of the existing computational methods for probe design and selection. We introduced the biological aspects of the problem and examined several issues related to the design and selection of probes: oligonucleotide fingerprinting, maximum distinguishing probe set, minimum cost probe set, and nonunique probe selection.


Integer Linear Programming True Cluster Cross Hybridization Candidate Probe Integer Linear Programming Formulation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Elisa Pappalardo
    • 1
  • Beyza Ahlatcioglu Ozkok
    • 2
  • Panos M. Pardalos
    • 3
  1. 1.Dipartmento di Matematica e InformaticaUniversita di CataniaCataniaItaly
  2. 2.Department of Mathematics, Faculty of Arts and ScienceYildiz Technical UniversityIstanbulTurkey
  3. 3.Department of Industrial and Systems EngineeringUniversity of FloridaGainesvilleUSA

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