Journal of Mathematical Biology

, Volume 70, Issue 6, pp 1327–1358 | Cite as

A combinatorial approach to the design of vaccines

  • Luis Martínez
  • Martin Milanič
  • Leire Legarreta
  • Paul Medvedev
  • Iker Malaina
  • Ildefonso M. de la Fuente
Article

Abstract

We present two new problems of combinatorial optimization and discuss their applications to the computational design of vaccines. In the shortest \(\lambda \)-superstring problem, given a family \(S_1,\ldots ,S_k\) of strings over a finite alphabet, a set \(\mathcal{T}\) of “target” strings over that alphabet, and an integer \(\lambda \), the task is to find a string of minimum length containing, for each \(i\), at least \(\lambda \) target strings as substrings of \(S_i\). In the shortest \(\lambda \)-cover superstring problem, given a collection \(X_1,\ldots , X_n\) of finite sets of strings over a finite alphabet and an integer \(\lambda \), the task is to find a string of minimum length containing, for each \(i\), at least \(\lambda \) elements of \(X_i\) as substrings. The two problems are polynomially equivalent, and the shortest \(\lambda \)-cover superstring problem is a common generalization of two well known combinatorial optimization problems, the shortest common superstring problem and the set cover problem. We present two approaches to obtain exact or approximate solutions to the shortest \(\lambda \)-superstring and \(\lambda \)-cover superstring problems: one based on integer programming, and a hill-climbing algorithm. An application is given to the computational design of vaccines and the algorithms are applied to experimental data taken from patients infected by H5N1 and HIV-1.

Keywords

Vaccine design Combinatorial Optimization Integer programming Hill-climbing Shortest common superstring problem Set cover problem 

Mathematics Subject Classification

68Q25 68W32 90C90 90C59 90C90 92C40 92C50 92D20 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Luis Martínez
    • 1
    • 2
  • Martin Milanič
    • 3
    • 4
  • Leire Legarreta
    • 1
    • 2
  • Paul Medvedev
    • 5
    • 6
    • 7
  • Iker Malaina
    • 2
    • 8
  • Ildefonso M. de la Fuente
    • 1
    • 2
    • 9
    • 10
  1. 1.Department of MathematicsUniversity of the Basque Country UPV/EHUBilbaoSpain
  2. 2.Biocruces Health Research Institute I.I.S. BiocrucesBasque CountrySpain
  3. 3.University of Primorska, UP IAMKoperSlovenia
  4. 4.University of Primorska, UP FAMNITKoperSlovenia
  5. 5.Department of Computer Science and EngineeringThe Pennsylvania State UniversityState CollegeUSA
  6. 6.Department of Biochemistry and Molecular BiologyThe Pennsylvania State UniversityState CollegeUSA
  7. 7.Genomic Sciences Institute of the HuckThe Pennsylvania State UniversityState CollegeUSA
  8. 8.Department of PhysiologyUniversity of the Basque Country UPV/EHUBilbaoSpain
  9. 9.Institute of Parasitology and Biomedicine López-NeyraCSICGranadaSpain
  10. 10.Unit of Biophysics (CSIC, UPV/EHU), and Department of Biochemistry and Molecular BiologyUniversity of the Basque CountryBilbaoSpain

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