title: GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs.
abstract: One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard have prompted the development of multiple new standards proposing different avenues to overcome these shortcomings. The lack of compatibility between standards, the compliance of parts with only some of the standards or even the type of constructs that each standard supports have significantly increased the complexity of assembling constructs from standardized parts. Here, we describe computer tools to facilitate the rigorous description of part compositions in the context of a rapidly changing landscape of physical construction methods and standards. A context-free grammar has been developed to model the structure of constructs compliant with six popular assembly standards. Its implementation in GenoCAD makes it possible for users to quickly assemble from a rich library of genetic parts, constructs compliant with any of six existing standards.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington St MC 0477, Blacksburg VA 24061, USA.
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Cai
authors.forename: Mandy L
authors.initials: ML
authors.lastname: Wilson
authors.forename: Jean
authors.initials: J
authors.lastname: Peccoud
mesh_terms: D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D005818:Genetic Engineering / Q000592:standards*; D012015:Reference Standards; D012984:Software
chemical_list: D004247:DNA