Easiest way to run BLAST, specifically blastn, against multiple databases

Question

[DavidStreid]

I would like to blastn a fasta file against 2-3 of the NCBI Blast Databases (e.g. search nt & ref_euk_rep_genomes at the same time). Is there a simple way to do this that doesn't require setting up a local BLAST database on my end?

After reviewing the BLAST UI instructions & toggling options on the UI, I can't seem to find a way to do this. A previous post mentioned this is possible w/ a local BLAST database, but this is time and resource intensive.

One final note - I would prefer not to limit my query to a set of organisms in case I miss the organism a read actually maps to. I have noticed in this case, I can still return very low E-values even when the correct organism isn't in my search space.

Thank you in advance for any help or advice.

Answer 1

[GenoMax]

AFAIK know there is no way to do this using BLAST web front end. You can create blast db aliases locally as the post you linked above shows.

[DavidStreid]

Understood - thank you!