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Title: A Formal Model for Databases in DNA
Authors: GILLIS, Joris 
Issue Date: 2012
Publisher: Springer-Verlag
Source: Horimoto, Katsuhisa; Nakatsui, Masahiko; Popov, Nicolaj (Ed.). Proceedings of Algebraic and Numeric Biology 2010, Springer-Verlag, p.18-37.
Series/Report: Lecture Notes in Computer Science
Series/Report no.: 6479
Abstract: 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 con- ventional 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.
Keywords: DNA Computing; Formal Model; Relational Algebra;DNA Computing, theoretical computer science, hybridization, graphs
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ISBN: 978-3-642-28066-5
DOI: 10.1007/978-3-642-28067-2_2
Category: C1
Type: Proceedings Paper
Appears in Collections:Research publications

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