1. What device would you like to connect to your computer?
As soon as you mentioned that the piece of software you have is designed to operate serial (COM) ports, this is, obviously, some sort of serial device, right?
2. Why do you need to use a USB cable in your configuration?
If your computer is short of physical COM ports, and you are searching for a way to connect a serial device to it, using a hardware device called USB to COM adapter would be a perfect solution.
USB to COM adapter is plugged into USB port of your computer, but appears in the system as a physical COM port. So you can plug in your serial device in the COM side of the adapter and work with it as with ordinary serial device.