Our goal is to better understand, at a theoretical level, the database aspects of DNA computing. Thereto, we introduce a formally defined data model of so-called sticker DNA complexes, suitable for the representation and manipulation of structured data in DNA. We also define DNAQL, a restricted programming language over sticker DNA complexes. DNAQL stands to general DNA computing as the standard relational algebra for relational databases stands to general-purpose conventional computing. The number of operations performed during the execution of a DNAQL program, on any input, is only polynomial in the dimension of the data, i.e., the number of bits needed to represent a single data entry. Moreover, each operation can be implemented in DNA using a constant number of laboratory steps. We prove that the relational algebra can be simulated in DNAQL. © 2012 Springer-Verlag Berlin Heidelberg.
CITATION STYLE
Gillis, J. J. M., & Van Den Bussche, J. (2012). A formal model for databases in DNA. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6479 LNCS, pp. 18–37). https://doi.org/10.1007/978-3-642-28067-2_2
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