Thread Subject: compare data from serial

Hi guys.
Can anybody help me in comparing my data from the serial port. The steps goes like this, I have send two data from the serial port from MCU(digital) to MATLAB then I want to graph the two data. I want to get the data from the serial port at an interval of .5seconds and flush the inputbuffer for the next update from the serial port data. I want to implement this because I want to send a command to my MCU after such time that the desired condition has been met. Thanks guys.