The Drupal MySQL database is often a performance bottleneck. Poorly configured MySQL limits the speed at which Drupal retrieves and stores data. If you have access to your server, then the best way to measure your MySQL performance is by running the MySQL Tuning Primer bash script for Linux. The configuration options are stored in a my.cnf file on your server.
There is also a Drupal module for anyone to use: the DB Tuner module, which is based off the Tuning Primer bash script. But you still need to tweak the my.cnf file manually and restart MySQL. Also, the slive erver should run at least 48hrs before testing.
Below are some resources for further information.
- Optimize your MySQL installation for Drupal