Hi @Dikaryon
Yes! Load up the target database and consider reformatting following our guide here (unless you have an NCBI* formatted > title lines in your fasta file).
You can use any fasta that you want to, just keep in mind that the content expectations in Galaxy are the same as they would be anywhere else this tool is used. See the BLAST guides for full details, and find some key details on each tool’s web form in Galaxy.
NCBI fasta formats are also accepted. These are very specific and invoke a bit of extra processing around how the identifiers are handled. These have brief references on the Galaxy tool form, so please see the link outs on the form to the NCBI web resources for the full details. You can also just try to see what happens! Any questions, you can share back a snippet of a few sequences, or better, your job/data through a shared history link, and we can probably help to clarify and troubleshoot.
If you have a larger sized query, creating an index of your custom genome target is a good idea. Find discussion about this also on the forms. In short, run the makeblastdb tool first to create an index, then use your custom index with the other BLAST tools.
Hope this helps! 