How do I set the off-target database for CRISPR?

The "Find CRISPR sites" function in Geneious Prime will search for off-target binding sites against a database of sequences. To do this, you will need to create a database of the sequences you wish to test against for off-target binding - this is typically the whole genome of your organism of interest, but can include other sequences, for example, the targeting vector.

To do this, you need to create a new empty folder in Geneious and import the sequences you want to test against into this folder. As there are a wide variety of genomes researchers may wish to test against; genome sequences can be very large; and new versions of genome assemblies may be released, Geneious does not contain inbuilt copies of any full genome sequences. Genomes can be downloaded directly from NCBI using the "NCBI" folders at the bottom of the Sources panel in Geneious (this is the panel on the left-hand side of Geneious). Commonly studied genomes (for example, the human, zebrafish and the rat genomes) can also be downloaded from NCBI using the links found in the "Genomes" folder in the "Sample Documents" in Geneious. Genomes can also be download from other sources and imported into Geneious using common file formats. This database of off-target sequences can be any size and can contain any sequences, although the larger this database is, the longer the search for CRISPR sites will take.

In the "Find CRISPR Sites" settings, click the button next to "Off-target database" and select the folder in Geneious containing the off-target sequences.

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