BIRCH
Local BLAST Databases
  Updating BLAST Databases

April  25, 2016


Databases in local BLAST database directory can be updated from BIRCH Administration Tool, which can be launched from the BIRCH launcher using File --> birchadmin, or from the command line by typing 'birchadmin'.

In birchadmin, choose UpdateAddInstall --> Install/Update files.

1) Choose the FTP site from which to download databases using the pull-down menu labeled "Download from". It is always best to choose the FTPsite that is geographically closest to your location.

2) Choose databases to update
By default, the Install/Update menu will update all installed databases.

The assumption is that it is most convenient to update all databases in a single job.

This menu also lets you choose which databases to update. A  [+] or [-] indicates, respectively, whether a database is already installed, or not. To add a database to the list of databases to update, choose Install/Update.
If you select a database that is not listed as being installed, that database will be downloaded. To prevent a database from being updated, select  "Do nothing." The current version will be retained in your BLASTDB directory.

Note that the databases are organized in to four tabs for Nucleotide, Protein, High-throughput or Other databases. Most of the "High-throughput" databases are nucleic sequences from high-throughput projects, such as ESTs, sequence-tagged sites. These databases tend to be quite large, with some exceptions. The one exception at this writing is Environmental - Protein. The other tab lists non-sequence databases, such as the taxonomy database, TaxDB. This is a small database, and includes taxonomy information needed for BLAST to identify species in BLAST reports, so it is probably useful to install this database.

To avoid unnecessary downloads, the dates of the local copies of each database file will be compared to those files at the FTP site. Files that are newer than the local copies will be downloaded, whereas files on the FTP site with older dates than the local copies will not be downloaded. Files that are found on the FTP site but not in the local BLAST database directory will also be downloaded. If you wish to force a download, first delete local copies of the databases, and the Add the new ones.

3) Launch the job
For all but the smallest databases, it will take anywhere from a few minutes to several hours to download each database. To begin the download, click on Run. The job will run in the background, meaning that you can quit BioLegato and logout if you wish during the download. If your system is configured to send email, you will receive a log of download progress by email, once all downloads are complete. The email will be sent to the BIRCH Administrator's email address, which was set when BIRCH was installed, and also appears on the BIRCH home page of your local copy of the documentation.
 
Note:  The [+]/[-] indicators in the Updte menu will not be updated to reflect addition of new databases until the next time you launch birchadmin after the download is completed.


At the command line - Suppose you wanted to update the Swissprot/Uniprot, vector and Taxonomy databases:

blastdbkit.py --update --dblist swissprot,vector,taxdb


blastdbkit --update --dblist all
Updates all currently-installed databases

Please send suggestions of comments regarding this page to psgendb@cc.umanitoba.ca.