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Usually we take mysql db/tables sql backup by mysqldump command or from phpmyadmin tool (my favorite). But if we need to take the binary backup, you can't do it . What you need to do, just simply copy all table files (*.frm, *.MYD, and *.MYI files). Usually these files are present in /var/lib/mysql directory in linux OS. If you want to check that you are getting the right data in tables you can use the following command

strings test.frm ,

say you are taking backup of test table. This command will show you all data in that table.

here's a useful link:
http://dev.mysql.com/doc/refman/5.0/en/backup.html