Have you tried optimizing and repairing the table in your MySQL database you are running WordPress on?
Your can manually do this with phpmyadmin:
http://support.hostgator.com/articles/specialized-help/technical/how-to-optimize-a-mysql-database-using-phpmyadmin
Or you can install a WordPress plugin such as WP Database Optimizer and set a regular optimization schedule:
http://wordpress.org/extend/plugins/wp-database-optimizer/
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