Slow MySQL Database - Restart Fixes Problem

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We're running MySQL v4.1 on RedHat Linux v3.  From time to time, queries
to the MySQL database start to execute very slowly (up to 15 minutes in
some cases).  When we restart the MySQL service, the queries fast again
(1 second or less).

Is there a way that I can optimize the MySQL installation such that this
restart is not required?

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