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This paper studies the use of profile alignment and support vector machines for subcellular localization. In the training phase, the profiles of all protein sequences in the training set are constructed by PSI-BLAST and the pairwise profile-alignment scores are used to form feature vectors for training a support vector machine (SVM) classifier. During testing, the profile of a query protein sequence is computed and aligned with all the profiles constructed during training to obtain a feature vector for classification by the SVM classifier. Tests on Reinhardt and Hubbard's eukaryotic protein dataset show that the total accuracy can reach 99.4%, which is significantly higher than those obtained by methods based on sequence alignments and amino acid composition. It was also found that the proposed method can still achieves a prediction accuracy of 96% even if none of the sequence pairs in the dataset contains more than 5% identity. This paper also demonstrates that the performance of the SVM is proportional to the degree of its kernel matrix meeting the Mercer's condition.