Genotype Specification Language.
Genotype Specification Language.
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基因型规范语言。
作者：
Erin H Wilson;Shiori Sagawa;James W Weis;Max G. Schubert;Mike Bissell;Brian Hawthorne;C. Reeves;Jed Dean;D. Platt
我们在此描述基因型规范语言 (GSL)，这种语言有助于快速设计用于工程基因组的大型且复杂的 DNA 构建体。 GSL 编译器实现了一种基于传统遗传符号的高级语言，以及一组低级 DNA 操作原语。该语言允许轻松地将来自克隆 DNA 构建体库和完全测序和注释基因组中的“自然”部分库的部分合并起来。 GSL 旨在让基因工程师使用他们的母语进行交流，同时为更高级别的抽象工具提供框架。为此，我们定义了四个语言级别，即 0 级（文字 DNA 序列）到 3 级，并增加了零件选择和构建路径的抽象性。 GSL 的目标是基于 DNA 切片的中间语言，可有效翻译为各种最终输出格式，例如 FASTA 和 GenBank，并包括指定指令和材料的格式，例如寡核苷酸引物，以允许单个菌株工程师或自动 DNA 组装核心设施物理构建 GSL 设计。
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.