Study sets are ways of grouping genomes in GenoSets. You can subject all of the genomes in the study set to the same analysis, or compare sets to each other.

We’re going to put all of our e. coli genomes in one study set to start off with, because we need to construct a script that sets up an all-against-all BLAST among them, and then run OrthoMCL to build the orthology information that allows us to perform content and function analysis.

In the project pane of your GenoSets window, select all of the available genomes.

Then right-click (or Control-click). A menu will appear, and you can choose “Create study set”. You’ll step through two dialogue windows – the first will only give you one option, “Create New” if you have no other study sets created. In the second window, you’ll need to name your study set in a way that’s informative to you, and you can also enter a description to help you keep track of what you were thinking when you created the study set.

Click Finish. Then choose the Study Sets tab in the top left pane of your main GenoSets window. You should now have an E. coli study set listed.