Can I use this tool with a custom database that I create and upload?
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! 
Ok great to hear. I have an already-formatted BLAST+ database, how would I get this into Galaxy?
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Hi @Dikaryon
You’ll need to load up the fasta for your database, then run makeblastdb in Galaxy. Any local index that you created cannot be loaded up to a public Galaxy server. These custom indexes are stored on the server and not really as a dataset in the history – your fasta file is instead used to create the index then a sort of placeholder is added to the history to provide the link. All of these are server specific.
There are two tools involved, and for small fasta files you can skip this step entirely and just use the fasta directly (the index is created at runtime as a single use disposable). All three use-case options are in the toggle at the top of BLAST+ forms, but please ask if you need more help choosing an option.
- Primary tool → NCBI BLAST+ makeblastdb Make BLAST database
- Optional formatting tool → NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb
If instead you are working at a server where you are the administrator, and you want to add your database as a native server index, that involves different methods. Do you need help with that?