By default, Geneious Prime will offer a BLAST algorithm most appropriate for the type of query sequence and type of database selected. The following algorithms are available:
When batch searching, all sequences will be compared using the same program against the same database.
Depending on the search program selected, you can change the search options by clicking on More Options. This will bring up program specific settings to allow you to further optimize your search. This is the expanded dialog for Megablast searches:
To ensure the results returned include only significant matches, the E value should be set on 1e-3 or less. E values higher than this may indicate that the match has occurred by chance. Changing the scoring table, word size and gap costs will also affect the number of hits returned and the aligned regions. For detailed information about these parameters, see the NCBI BLAST Help.
It is possible to restrict the results of a BLAST search to a specific species, or to exclude certain types of sequence by using an Entrez query in the advanced options. For example, to only return results from mouse, enter Mus musculus[organism] in the Entrez query field. To remove results that come from uncultured, unclassified, or environmental samples you can use all[filter] NOT uncultured[filter] NOT "environmental"[filter] NOT unclassified[filter].
For further examples of Entrez query terms, see here.
You may also be interested in running BLAST searches on your own computer and making your own databases to search against. You can add a local BLAST service from the BLAST dialog by clicking the Add/Remove Databases button and selecting Set Up BLAST Services. This will then guide you through installing BLAST. You will then be able to add searchable databases from downloaded sequence files, or from selected sequences within Geneious. This is a convenient way of maintaining a specialist sequence set to compare sequences against.