How to incorporate the sequence order effect is a key and logical step for improving the prediction quality of protein subcellular location, but meanwhile it is a very difficult problem as well. This is because the number of possible sequence order patterns in proteins is extremely large, which has posed a formidable barrier to construct an effective training data set for statistical treatment based on the current knowledge. That is why most of the existing prediction algorithms are operated based on the amino-acid composition alone. In this paper, based on the physicochemical distance between amino acids, a set of sequence-order-coupling numbers was introduced to reflect the sequence order effect, or in a rigorous term, the quasi-sequence-order effect. Furthermore, the covariant discriminant algorithm by Chou and Elrod (Protein Eng. 12, 107-118, 1999) developed recently was augmented to allow the prediction performed by using the input of both the sequence-order-coupling numbers and amino-acid composition. A remarkable improvement was observed in the prediction quality using the augmented covariant discriminant algorithm. The approach described here represents one promising step forward in the efforts of incorporating sequence order effect in protein subcellular location prediction. It is anticipated that the current approach may also have a series of impacts on the prediction of other protein features by statistical approaches.