Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays

  • Ion I. Măndoiu
  • Claudia Prăjescu
  • Dragoş Trincă
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3680)


In this paper we address two optimization problems arising in the design of genomic assays based on universal tag arrays. First, we address the universal array tag set design problem. For this problem, we extend previous formulations to incorporate antitag-to-antitag hybridization constraints in addition to constraints on antitag-to-tag hybridization specificity, establish a constructive upper bound on the maximum number of tags satisfying the extended constraints, and propose a simple alphabetic tree search tag selection algorithm. Second, we give methods for improving the multiplexing rate in large-scale genomic assays by combining primer selection with tag assignment. Experimental results on simulated data show that this integrated optimization leads to reductions of up to 50% in the number of required arrays.


Reporter Probe Prime Pool Genomic Assay Extended Constraint Universal Array 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

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

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