Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.
BACKGROUND
Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains.


RESULTS
Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language.


METHODS
The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.
Virginia Bioinformatics Institute, Department of Plant Pathology, Physiology, and Weed Science and ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA.
Mandy L
ML
Wilson
Sakiko
S
Okumoto
Laura
L
Adam
Jean
J
Peccoud
D020121:5' Untranslated Regions / Q000235:genetics; D000465:Algorithms; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D005822:Genetic Vectors / Q000235:genetics*; D018745:Genome, Plant; D009876:Operon; D011995:Recombination, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software
D020121:5' Untranslated Regions