In a previous video, we went through the basics of how to design DNA constructs using the design wizard in GenoCAD. The design wizard guides GenoCAD users through the design process using genetic grammars and their associated parts libraries. In this video, we will walk through how to develop a simple grammar from scratch.
First, click on “Parts and Grammars.” To get to the grammar editor, we need to click on the “grammar” tab. To create a new grammar, we need to click on the “Add/Import Grammar” button. Now we can give our grammar a name, describe what it is used for and select an appropriate set of icons. For this demo, we’ll use the Synthetic Biology Open Language visual icons.
We could also import a GenoCAD grammar if we had one available.
In the grammar editor, there are three main sections: the parts categories, the category details and the category rules. Let’s start by adding in some categories for a basic gene expression cassette. Each category is assigned a letter or letters and a name. Categories can also be given descriptions, GenBank qualifiers and appropriate icons. Here we will make 5 categories: a “cassette” category, a “promoter” category, a “ribosome binding site” category, a “protein coding sequence” category and a “transcriptional terminator” category.
Now that our categories have been added, we can begin to structure our grammar. The first step of making any grammar in GenoCAD is to begin with the “Start” category. Here we will make two child rules from the Start category: one that goes to a single cassette and another that goes to two cassettes. Let’s test this to make sure.
Now we will define the rules for the structure of our cassette. Let’s add a child rule to our Cassette category so that it goes to a promoter, RBS, coding sequence and terminator – in that order. Testing this shows that our grammar is doing what we want it to.
And that’s how easy it is to make a grammar in GenoCAD.