Improved Lower Bounds for Constant GC-Content DNA Codes

DOI10.1109/TIT.2007.911167MaRDI QIDQ3604560zbMATH OpenFDO

Authors Yeow Meng Chee, San Ling

Publication date 24 February 2009

Published in IEEE Transactions on Information Theory (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0803.3657

zbMATH Keywords

stochastic local searchexhaustive searchDNA codesHamming distance modeloligonucleotide libraries

Mathematics Subject Classification ID

Information storage and retrieval of data (68P20) Protein sequences, DNA sequences (92D20) Bounds on codes (94B65) Other types of codes (94B60)

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. We introduce a new stochastic local search method which yields improvements up to more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. We also found several optimal libraries by computing maximum cliques on certain graphs.

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