Updating the BLAST Database: update_BLASTDB

This utility updates the BLAST database from a copy on the Schrödinger web site that is synchronized nightly with the BLAST web site, or via FTP from the NCBI web site. The preformatted database files are downloaded. The syntax is:

$SCHRODINGER/utilities/update_BLASTDB [options] 

For a description of the options, run the command with the -h option, or see update_BLASTDB Command Help.

The default behavior for this utility will skip updating the local nonredundant database. To update the nonredundant database, use the -include_nr option. Note that you will need to have the proper permissions to the BLAST database being updated for the script to function.

The BLAST database is installed in the first location found in the following list:

• The location specified by the -f option.
• $PSP_BLASTDB
• $SCHRODINGER_THIRDPARTY/database/blast
• $SCHRODINGER/thirdparty/database/blast

The environment variables are described in Setting Environment Variables for the Prime Third-Party Software and Databases.