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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. Where your BLAST databases are located can be seen in the "BLAST Database Manager" tool.
BLAST Data Manager manual page: https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Manage_BLAST_databases.html
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).
An example
If saved as "example.nal", the following nal file content between the dotted lines, will create a database called "example" with description "My bunch of databases" by combining the three existing databases NG_005905, NG_012772, and SequenceList.
nal file:
---------------------------------------------------------------------
#
# my comments: merging three databases
#
TITLE My bunch of databases
DBLIST "NG_005905" "NG_012772" "SequenceList"
---------------------------------------------------------------------
In the BLAST Database Manager it can be check if this approach created that new database and if the number of sequences per data base add up to be the number fo sequences for the new database.
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