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mySQL CPU Usage 99%

We have a java based SaaS application running on mySQL database on a 2 GB Linux VPS. Recently we added RAM to the server and since couple of days, mySQL is taking up 99% of CPU usage. We are quite clueless as to why this is happening. We have made some changes in the my.cnf file as we have read in certain forums. We have enhanced the resources for mySQL. Please help.

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