For any two devices to transmit data to each other they need to agree on some sort of format so they can understand what the other one is saying. A protocol is an agreed-upon format for transmitting data between two devices. The protocol determines the type of error checking to be used, the data compression method, if any, how the sending device will indicate that it has finished sending a message, and how the receiving device will indicate that it has received a message.
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A protocol also describes the format a given message must take within the context of a particular activity such as sending e-mail, establishing remote connections, file transfer, etc. Using a given protocol ensures that the data sent between the computers involved are correctly formatted and transmitted, and in some particular cases, are pre-defined queries and responses.
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Developers can choose from a variety of common protocols such as HTTP , FTP, POP, SMTP, TCP/IP etc. Each has particular advantages and disadvantages; for example, some are simpler than others, some are more reliable, some are faster, etc. Which protocol to use also depends upon what the developer is trying to do; using an e-mail protocol when a file transfer is desired would not be appropriate.
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The only real concern a user has about any protocol is that the user's computer or device supports the right ones if the user wants to communicate with other computers. The protocol can be implemented either in hardware or in software.
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