Exact and Approximation Algorithms for DNA Tag Set Design

  • Ion I. Măndoiu
  • Dragoş Trincă
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3537)

Abstract

In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these formulations can be solved to optimality for instance sizes of practical interest by using general purpose optimization packages. Second, we note the benefits of periodic tags, and establish an interesting connection between the tag design problem and the problem of packing the maximum number of vertex-disjoint directed cycles in a given graph. We show that combining a simple greedy cycle packing algorithm with a previously proposed alphabetic tree search strategy yields an increase of over 40% in the number of tags compared to previous methods.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Ion I. Măndoiu
    • 1
  • Dragoş Trincă
    • 1
  1. 1.CSE DepartmentUniversity of ConnecticutStorrsUSA

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