from: https://secure.clcbio.com/helpspot/index.php?pg=kb.page&id=113

Can I run a local BLAST search again multiple blast databases simultaneously? (blast, blastn, blastp, blastx, serveral databases)
By default, you will be offered single BLAST databases to search via the CLC Workbench BLAST interface.

By creating a simple text file outside the Workbench, and saving it the appropriate location, you can search multiple databases in a single search. To do this:

1) Create a text file and name it with the suffix .nal if your databases were created from nucleotide sequences, or the suffix .pal if your databases were created from peptide sequences.

Attached is a file showing the type of format this file should take. Just replace the names of the databases in that file (which are in quotes), with the names of databases you wish to use. You can add as many databases to that list as you like, just as long as you keep the same type of formatting as in the example file.

2) Put this file into the same folder on your system as your databases are stored in.

Please note that steps 1 and 2 are done outside the Workbench.

Now, when you go to run a search using your Workbench, one of the databases offered to you for blastn, blastx or tblastx should be the same name of the .nal file you created (but without the .nal suffix). If you run a blastp or tblastx search, then one of the databases offered to you should have the same name as the .pal file you created (but without the .pal suffix).

example.nal

#
# Alias file created 11/21/2011 16:25:58
#
TITLE My bunch of databases
DBLIST "bigstaticdatabase" "smalldynamicdatabase"

Can I run a local BLAST search again multiple blast databases simultaneously?