Combinatorial Algorithms for Design of DNA Arrays

  • Sridhar Hannenhalli
  • Earl Hubbell
  • Robert Lipshutz
  • Pavel A. Pevzner
Part of the Advances in Biochemical Engineering/Biotechnology book series (ABE, volume 77)


Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination (border length minimization problem) and reducing the complexity of masks (mask decomposition problem). We describe algorithms that reduce the number of rectangles in mask decomposition by 20–30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.


DNA arrays Photolitography Mask design Combinatorial algorithms Rectangle cover problem 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Sridhar Hannenhalli
    • 1
  • Earl Hubbell
    • 2
  • Robert Lipshutz
    • 2
  • Pavel A. Pevzner
    • 3
  1. 1.Departments of MathematicsUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.AffymetrixSanta ClaraUSA
  3. 3.Departments of Computer Science and EngineeringUniversity of California at San DiegoLa JollaUSA

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