GoDaddy is really the worst host that I've seen; they're great for domain names, but are not suited to handle anything more than basic websites.
When your database gets larger, it becomes more and more unsafe to use phpMyAdmin or any PHP-based backup scripts, as they tend to timeout - leaving you with an incomplete or corrupted backup. The same also applies to restores.
As daPLAYBOY suggested, you could try BigDump; but I know that GoDaddy doesn't have cPanel.
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