  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 greedy 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.
