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The functions of proteins are closely correlated with their subcellular localizations. Based on the concept of pseudo amino acid composition, the nonlinear energy operator (NEO) approach is introduced to incorporate the sequence order effect on protein subcellular localization. Results obtained through self- consistency, jackknife and independent dataset tests indicate that the prediction accuracies by the current algorithm are significantly higher than those by using conventional 20 D amino acid components. It is anticipated that some signal processing approaches, such as nonlinear energy operator, may serve as useful vehicles in biologic area.