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What communication protocols are used to communicate with probes that are many light minutes or even hours away?

Not only the signal will be weak and badly damaged by background noise, we can't just go confirming each packet upon receiving it, or demanding a resend; time windows are limited (radio antennas on Earth facing given probe), and there's a plenty of data to be sent - plus broadcasting that from the probe towards Earth costs precious energy too.

Surely the hardware plays a big role in getting as little losses as possible but what protocols handle this kind of transmission and how do they improve the communication - what mechanisms do they use to handle the problems?

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