Generating DNA code words using forbidding and enforcing systems
Research in DNA computing was initiated by Leonard Adleman in 1994 when he solved an instance of an NP-complete problem solely by molecules. DNA code words arose in the attempt to avoid unwanted hybridizations of DNA strands for DNA based computations. Given a set of constraints, generating a large set of DNA strands that satisfy the constraints is an important problem in DNA computing. On the other hand, motivated by the non-determinism of molecular reactions, A. Ehrenfeucht and G. Rozenberg introduced forbidding and enforcing systems (fe-systems) as a model of computation that defines classes of languages based on two sets of constraints. We attempt to establish a connection between these two areas of research in natural computing by characterizing a variety of DNA codes that avoid certain types of cross hybridizations by fe-systems. We show that one fe-system can generate the entire class of DNA codes of a certain property, for example θ-k-codes, and confirm some properties of DNA codes through fe-systems. We generalize by fe-systems some known methods of generating good DNA code words which have been tested experimentally. © 2012 Springer-Verlag.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Digital Object Identifier (DOI)
Genova, & Mahalingam, K. (n.d.). Generating DNA Code Words Using Forbidding and Enforcing Systems. In Theory and Practice of Natural Computing (pp. 147–160). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33860-1_13