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You can actually change a lot of the my.cnf parameters through the API (as well as through the std mysql protocol from a command line client), so you can adapt settings for your needs. Overall the memory size of buffers and caches are already pre-set for you by AWS, but in the end, they don't act as a DBA who would tune the database for you in any way. If the DB is slow, it's up to you to figure out what to do, or if you're transforming huge tables (like adding a column) you still need someone who knows all the tricks for doing this effectively with mysql. All these things get into the application domain...