Besides the databases that are part of the default configuration, you can add more databases located at NCBI by configuring files in the Workbench installation directory.
The list of databases that can be added is here: https://web.archive.org/web/20120409025527/http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html.
In order to add a new database, find the
settings folder in the Workbench installation directory (e.g.
C:\Program files\CLC Genomics Workbench 4). Download unzip and place the following files in this directory to replace the built-in list of databases:
- Nucleotide databases: https://resources.qiagenbioinformatics.com/wbsettings/NCBI_BlastNucleotideDatabases.zip
- Protein databases: https://resources.qiagenbioinformatics.com/wbsettings/NCBI_BlastProteinDatabases.zip
Open the file you have downloaded into the
settings folder, e.g.
NCBI_BlastProteinDatabases.properties in a text editor and you will see the contents look like this:
nr[clcdefault] = Non-redundant protein sequences refseq_protein = Reference proteins swissprot = Swiss-Prot protein sequences pat = Patented protein sequences pdb = Protein Data Bank proteins env_nr = Environmental samples month = New or revised GenBank sequencesSimply add another database as a new line with the first item being the database name taken from https://web.archive.org/web/20120409025527/http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html and the second part is the name to display in the Workbench. Restart the Workbench, and the new database will be visible in the BLAST dialog.