You can BLAST to a local copy of a preformatted BLAST database from NCBI using custom BLAST in Geneious.
To set up the BLAST executables, go to Tools→Add/Remove Databases→Set Up BLAST Services→Custom BLAST. Check "Let Geneious do the setup" and click OK. Your BLAST folder should be created inside your Geneious Data folder, which is normally located in your User directory.
Preformatted NCBI BLAST databases are available from this link https://ftp.ncbi.nlm.nih.gov/blast/db/. These databases include most of the databases that you can BLAST to using the NCBI BLAST function in Geneious, such as nr/nt, EST, refseq, 16S Microbial and environmental samples.
To use the preformatted databases with your custom BLAST installation in Geneious, download the tar.gz files and uncompress the files. Each tar.gz file contains 8 files, and these must be put in the BLAST/data folder that was created in your Geneious Data folder when you set up custom BLAST. The screenshot below shows an example of the extracted NCBI 16S Microbial database files in the custom BLAST data folder.
Then restart Geneious, and the preformatted database should now show up in the list of custom BLAST databases when you click BLAST.
If the database you wish to use has multiple volumes (for example refseq_genomic.00, refseq_genomic.01 etc). Then you must download and extract all volumes. These files must all go directly in the BLAST/data folder, not in a subfolder. Within the extracted files, there will be a file with the suffix .pal or .nal. This file is required to link the individual volumes into a single database (only one copy of the file is required).
Note that due to the large size of the nr and nt databases we do not recommend attempting to BLAST to a local copy of these databases on a standard personal computer. You will find that it is many times slower than NCBI, as at NCBI the BLAST computation is split across potentially 1000s of cores on a high performance server. As an alternative, we suggest setting up cloud BLAST on an AWS EC2 instance. This post provides instructions on linking to cloud BLAST from Geneious Prime.