mtop or MySQL top command shows the MySQL commands consuming the greatest time.It is a command similar as top which provides a dynamic real-time view of a running system. Top can display system summary information as well as a list of tasks currently being managed by the Linux kernel.Difference is that mtop show only the MySQL tasks.
Normally, run as a console program this will allow you to see slow or badly optimized queries as they will stay on the screen for a while. However, if you are hunting for short lived queries, running in the manualrefresh mode with a short refresh time will allow you to catch short lived queries as well.
Installing mtop
sudo apt-get install mtop