The present invention provides a method of empirical analysis of metabolic pathways using a cell-free system of microalgae for a more efficient and high-performance gene function analysis of the microalgae, the method comprising: a microalgae homogenate preparation step for preparing a microalgae homogenate; a step of treating an effector molecule after loading the microalgae homogenate in a reaction vessel; and a step of comparing the effector molecule with an untreated control group and measuring biological effects according to the treatment of the effector molecule.
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