Download NCBI pre-formatted BLAST databases

Many popular pre-formatted databases are available for download from the NCBI. You can download any of the databases available from the list at from within your Workbench.

You must be connected to the internet to use this tool.

To download a database, go to:

        Toolbox | BLAST (Image blastsearch)| Download BLAST Databases (Image download_from_web_16_h_p)

A window like the one in figure 16.13 pops up showing you the list of databases available for download.

Image NCBIpreformattedblastdbs1
Figure 16.13: Choose from pre-formatted BLAST databases at the NCBI 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.

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.