Combinatorial Enumeration
Linear constructions for DNA codes
Theoretical Computer Science
Bounds and constructions for ternary constant-composition codes
IEEE Transactions on Information Theory
Hardware acceleration of multi-deme genetic algorithm for the application of DNA codeword searching
Proceedings of the 9th annual conference on Genetic and evolutionary computation
Linear size optimal q-ary constant-weight codes and constant-composition codes
IEEE Transactions on Information Theory
An information security-based literature survey and classification framework of data storage in DNA
International Journal of Networking and Virtual Organisations
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In this paper, we describe a broad class of problems arising in the context of designing codes for DNA computing. We primarily focus on design considerations pertaining to the phenomena of secondary structure formation in single-stranded DNA molecules and non-selective cross-hybridization. Secondary structure formation refers to the tendency of single-stranded DNA sequences to fold back upon themselves, thus becoming inactive in the computation process, while non-selective cross-hybridization refers to unwanted pairing between DNA sequences involved in the computation process. We use the Nussinov-Jacobson algorithm for secondary structure prediction to identify some design criteria that reduce the possibility of secondary structure formation in a codeword. These design criteria can be formulated in terms of constraints on the number of complementary pair matches between a DNA codeword and some of its shifts. We provide a sampling of simple techniques for enumerating and constructing sets of DNA sequences with properties that inhibit non-selective hybridization and secondary structure formation. Novel constructions of such codes include using cyclic reversible extended Goppa codes, generalized Hadamard matrices, and a binary mapping approach. Cyclic code constructions are particularly useful in light of the fact we prove that the presence of a cyclic structure reduces the complexity of testing DNA codes for secondary structure formation.