15.1 Setting up a BLAST search

To run a BLAST search in Geneious Prime, select your query sequence or sequences and click the BLAST button in the toolbar. This operation can also be accessed by going to the Tools menu or by right-clicking (Ctrl+click on Mac OS X) on a sequence document and choosing BLAST. You can choose to BLAST either your currently selected sequence documents or a sequence you enter manually. If you choose to enter your sequence manually, then Geneious will display a large text box in which you can enter your query sequence as either unformatted text or FASTA format.


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Figure 15.1: BLAST Options


Select your database using the first drop-down box. Databases are grouped together under their respective services. Then choose which kind of BLAST search you wish to run under Program. The available programs will depend on the database you have chosen.

Geneious Prime can perform seven different kinds of BLAST search:

Three options are available for displaying your results:

You can also specify how much of each matching sequence to retrieve from your database:

Geneious also allows you to specify most of the advanced options that are available in BLAST. To access the advanced options click the More Options button which is in the bottom left of the BLAST options. The available options vary depending on the kind of BLAST search you have selected. For details on each of the options you can hover your mouse over the option to see a short description or refer to the BLAST documentation from NCBI.