Genotype Specification Language

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• 作者：Erin H. Wilson ; Shiori Sagawa ; James W. Weis ; Max G. Schubert ; Michael Bissell ; Brian Hawthorne ; Christopher D Reeves ; Jed Dean ; Darren Platt
• 刊名：ACS Synthetic Biology
• 出版年：2016
• 出版时间：June 17, 2016
• 年：2016
• 卷：5
• 期：6
• 页码：471-478
• 全文大小：406K
• 年卷期：0
• ISSN：2161-5063

文摘

We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the “natural” library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.