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Neoagaro-oligosaccharides (NAOS) have health benefits that are related to their amount and degree of polymerization (DP). However, the current methods that are used to quantify enzymatically released NAOS are un-specific and time-consuming. Agar has been extracted from Gelidium amansii and has been degraded by AgaXa (a recombinant β-agarase). Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) has been adapted in order to quantify NAOS. In addition, the anti-oxidant activity of the degraded samples has been assessed. We have found that the PACE method provided sensitive, precise, and accurate quantification for each of the six NAOS samples. PACE has revealed that the DP of the enzymatic products from the AgaXa digestion were mainly neoagaro-octaose and neoagaro-decaose. The degraded samples exhibited increased radical-scavenging activity towards 2,2-diphenyl-1-picrylhydrazyl and 2,2-azino-bis(3-ethylbenzothiazoline sulfonic acid) radicals. While the anti-oxidant activity may have been from NAOS activity and contributions from neoagaro-octaose and neoagaro-decaose. The adapted PACE method that has been presented here is promising for large sample analysis during quality control and for characterizing novel β-agarase degradation mechanisms. [ABSTRACT FROM AUTHOR]