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The best way to design a database is first to find out all entities and All attributes of a entity and relationship between them.Then make table according to your entity and columns according to its attributes and maintain relationship using foreign keys.
First major difference I see is that InnoDB implements row-level lock while MyISAM can do only a table-level lock. You will find better crash recovery in InnoDB. However, it doesn't haveFULLTEXTsearch indexes until v5.6, as does MyISAM. InnoDB also implements transactions,foreign keys and relationship constraints while MyISAM does not.
