MySQL Server can be optimized at a basic level, using the MySQL tuner script.

Download the script using the command:

wget https://github.com/major/MySQLTuner-perl/zipball/master

Now, run the commands:

unzip master

cd major-MySQLTuner*

chmod +x mysqltuner.pl

perl mysqltuner.pl

The script will check the status of MySQL and update you with the variables that you need to tweak to optimize MySQL.

Variables to adjust:
query_cache_size (> 64M)
join_buffer_size (> 2.0M, or always use indexes with joins)
tmp_table_size (> 16M)
max_heap_table_size (> 16M)
table_open_cache (> 8192)
innodb_buffer_pool_size (>= 520M)

These you can change by editing /etc/my.cnf file, that make mysql perform better.