Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks

Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matc...

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Bibliographic Details
Published inACS synthetic biology Vol. 1; no. 8; pp. 332 - 344
Main Authors Yaman, Fusun, Bhatia, Swapnil, Adler, Aaron, Densmore, Douglas, Beal, Jacob
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 17.08.2012
Subjects
Algorithms
DNA - genetics
Gene Regulatory Networks
Models, Genetic
Software
Synthetic Biology - statistics & numerical data
part matching
signal matching
abstract genetic regulatory network
feature matching
MatchMaker
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Summary:Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps.
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ISSN:2161-5063
2161-5063
DOI:10.1021/sb300032y