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Is it possible to patent a communication protocol, like HTTP or IMAP or SMTP, etc..?

How about a sequence of REST APIs?

If not, is there anyway to prevent others developing clone applications that will be compatible with my application?

If yes, any pointers to a similar patent would be highly appreciated.

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Last year the answer for protocols was yes. It might still be yes at the USPTO but now it is likely for a judge with no technical background to say "it is just doing what computers do". APIs have not been found patentable but they are copyrightable - unless the case that Google wants to take to the Supreme Court goes the other way. Some links. PatentlyO on Google vs Oracle/Sun, PatentlyO on are API's patentable or copyrightable.

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