Many popular pre-formatted databases are available for download from the NCBI. You can download any of the databases available from the list at ftp://ftp.ncbi.nlm.nih.gov/blast/db/ from within your Workbench.
You must be connected to the internet to use this tool.
To download a database, go to:
Toolbox | BLAST ()| Download BLAST Databases ()
A window like the one in figure 13.13 pops up showing you the list of databases available for download.
In this window, you can see the names of the databases, the date they were made available for download on the NCBI site, the size of the files associated with that database, and a brief description of each database. You can also see whether the database has any dependencies. This aspect is described below.
You can also specify which of your database locations you would like to store the files in. Please see the Manage BLAST databases.
There are two very important things to note if you wish to take advantage of this tool.
- Many of the databases listed are very large. Please make sure you have space for them. If you are working on a shared system, we recommend you discuss your plans with your system administrator and fellow users.
- Some of the databases listed are dependent on others. This will be listed in the Dependencies column of the Download BLAST Databases window. This means that while the database your are interested in may seem very small, it may require that you also download a very big database on which it depends.
An example of the second item above is Swissprot. To download a database from the NCBI that would allow you to search just Swissprot entries, you need to download the whole nr database in addition to the entry for Swissprot.