Serial data acquisition and framing

Hello, all.
I need to acquire data from two serial ports, search for sync words and frame them. The data length is 32 bytes arriving 25 times per second from both ports. I need to frame them. I am using matlab script to frame them but it sometimes misses the incoming data. I think the data rate is not too much, labview can handle it easily.
       Is the matlab script slowing it down? what can be the efficient way of framing the data.
Thanking in anticipation.

What do you mean by "framing the data"?  Give some examples.  I'm sure matlab scripts are going to run slower than native LabVIEW code.

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