Speed up a wordpress site is not a MySQL settings issue. One site in order to perform well is to USE MySQL with the best efficient way (limit your queries results, get only what you need)
Default wordpress database schema have been already set up (primary keys, indexes e.t.c) to be used by the default scripts (e.x. WP_Query) with the more efficient way.
The best thing to do if you own a low performance wp site is to check the server itself (you can install many plugins to monitor you php and mysql performance) and if you are pretty sure that is not a script issue that causes the latency then contact with your hosting provider in order to check your machine.
Now if you are using custom queries in your wordpress installation you must always have in mind the default db schema because it is very easy to create a slow (sometimes very slow) custom query.
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