By experience, most of a website’s performance issues are database related, if code and queries are already optimized. Tom has an interesting post about optimizing your MySQL database. The issue isn’t related to optimizing queries, but the server itself, and the techniques used to reduce execution time of a heavy query from 15 minutes to 1~3 minutes !
MySQL RDBMS is not a real RDBMS system but it has got a lot of similarities like any of them. MySQL has a configuration file called my.cnf (usually placed under the /etc folder of the Linux box).
In my example, I had a heavy query which took almost 90% of the CPU performance for more than 15 minutes… no RAM was improperly used, and no buffers were altered during these 15minutes. I succeeded in reducing the query time to 1 ~ 3 minutes…
