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Chiral separation or separation of racemic chemicals is very important in pharmaceutical development because of the different pharmacological and toxicological properties of each enantiomer. Capillary electrophoresis (CE) is an important analytical technique used in chiral separations, due to its advantages like high resolution, high speed and low consumption of chemical reagents. Tropomyosin present in mollusk species is the most common allergen in humans and causes excessive immune responses. To simultaneously detect tropomyosin allergens in mollusk species, a multiplex PCR assay combined with capillary electrophoresis was developed for the detection of tropomyosin genes of oyster, mussel, abalone, and clam, and the 18S rRNA gene of eukaryotes.