Abstract
The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA computing, DNA microarray technologies, and molecular bar coding. Various techniques have been studied for the construction of such oligonucleotide libraries, ranging from algorithmic constructions via stochastic local search to theoretical constructions via coding theory. A new stochastic local search method is introduced, which yields improvements for more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. Several optimal libraries are also found by computing maximum cliques on certain graphs.