Yaman Fusun, Bhatia Swapnil, Adler Aaron, Densmore Douglas, Beal Jacob
Raytheon BBN Technologies, 10 Moulton St., Cambridge, MA, USA.
ACS Synth Biol. 2012 Aug 17;1(8):332-44. doi: 10.1021/sb300032y. Epub 2012 Jul 25.
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.
提高合成生物学设计的抽象层次需要解决几个具有挑战性的问题，包括将抽象设计映射到DNA序列。在本文中，我们提出了首个解决此问题的形式体系和算法。这种转换的关键步骤是特征匹配、信号匹配和部件匹配。特征匹配确保映射满足抽象设计中的调控关系。信号匹配确保功能单元的表达水平兼容。最后，部件匹配找到一个能够实现该设计的DNA部件序列。我们的软件工具MatchMaker实现了这三个步骤。
