The most efficient way I have found to backup my databases on my Cpanel Linux system is using a MySQL dump via a cron job.
Here is the syntax:
/usr/bin/mysqldump -u username -ppassword databasename | gzip -c > /home/Digitize Design/public_html/_db_backups/`date "+\%Y\%M\%d\%H\%m"`.filename.sql.gz
All you need to do is replace "username", "password", "databasename", and the location of where to save the file. As you can probably tell it will also gzip the backup to save disk space.
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