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Is it possible to custom program an AVR chip by putting it in the AVR socket of an Arduino?

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Yes. You can program a virgin AVR by connecting it up to some GPIOs and reflashing it. If you had a second Arduino, the chip being programmed would sit in the socket.

http://arduino.cc/en/Tutorial/ArduinoISP

(With the Arduino Uno, it's more complex it seems)

Can you use an Arduino Uno as an ATMega328 Programmer?

How to burn atmega328 chip via Arduino UNO as ISP?

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If you have an Arduino with a FT232RL chip onbaord (Arduino Duemilanove or earlier models or their clones) then you can bitbang the FT232RL to program the bootloader or any other code into the AVR.

http://make.kosakalab.com/arduino/bootloader/index_en.html

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