NCBI BLAST Databases

This is the landing page for the NCBI BLAST databases which contains examples, tutorials and other information for the use of these databases on the UFS HPC.

Dataset information

The UFS HPC currently mirrors the databases provided by the NCBI (https://ftp.ncbi.nlm.nih.gov/blast/db/) on the UFS software mirror (http://mirror.ufs.ac.za/blast/)

To make the databases locally accessible to researchers for use with BLAST+ or other applications, we have conveniently wrapped the databases in an environmental module which users can load.

The following databases are availible:

  • nr
  • nt
  • refseq_protein
  • swissprot

Databases from the NCBI collection are added based on need (they are very large). Thus if you need to use a database not in the list above, you may request its inclusion by contacting the HPC staff at hpc@ufs.ac.za

Dataset updating policy

Update Interval

The databases will be updated automatically every 3 months. Users may request an earlier update by contacting the HPC staff at hpc@ufs.ac.za. Note that all users will be notified via email if an earlier update is performed.

Available versions

Two versions of the databases will be available on a rolling model:

  • The most recently updated version (loaded via blast/current)
  • The previously updated version (loaded via blast/previous)

Note that if an update is performed, the current version of the database will become the previous version and the version after the update will become the current version.

To check the time stamp of when the currently loaded database was updated, you may issue the following command: 

    $ blastdbcmd -info -db nt | blastdb_date

Please note the following regarding the command above:

  1. nt is used in the example, but you may replace it with the particular database for which you want to confirm the creation date
  2. The specific day and time may differ between the different databases in the collection. Thus do not be alarmed - only the month and year need to match (to indicate that they come from the same set).

Version freeze

If the same version of the database is required for longterm project, this may be accomplished by cloning the current version of the database to the user's home directory.

Please note that this should only be done if absolutely necessary as the NCBI databases are very large and consumes a large amount of diskspace.

To clone a database to your home directory, follow these steps:

UFS HPC usage example

UFS HPC Community Guides and Tutorials

Official site and documentation

Licensing Information

The BLAST databases are publicly available and free to use

External Guides and Resources

  • No external guides are availible.
  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za