HomeCLC FAQ - Import, export, and downloadsDownload toolsWhy are no BLAST databases listed in the Download BLAST Databases window?

4.2. Why are no BLAST databases listed in the Download BLAST Databases window?

The tool in the CLC Workbenches at:

Toolbox | BLAST | Download BLAST Databases

connects to a site at the NCBI:

ftp://ftp.ncbi.nlm.nih.gov/blast/db/

where they make pre-formatted BLAST databases available. This means that you must be able to connect to the external network from the machine that the CLC Workbench is running on  and if there is a proxy at your site, the Workbench must be configured to use the relevant proxy information.

If your machine is unable to connect the external network, and specifically to the ftp site above, then the "Download BLAST Database" window will not have any content.

Instructions for how to configure the Workbench with proxy information can be found in our manual at:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Network_configuration.html

You may need to talk to a local IT person to find what the correct settings are for your site.

If connecting to the external network is not possible on the machine the Workbench is installed on, you could download pre-formatted databases on another machine and put them in a CLC database location, or you can create your own BLAST databases. These are described in our manual at:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Make_pre_formatted_BLAST_databases_available.html

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_local_BLAST_databases.html

 

Please note that the nt and nr databases from the NCBI are very big. If these are the databases you wish to search against, it will be best to download the pre-formatted database files rathe than attempting to build these databases yourself. You may also wish to check out if others at your site are already making the relevant BLAST databases available for searching so you do not have to download and store the database yourself.

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