Subcellular localization is a key characteristic of protein functional research. Proteins are transported to specific compartment after they are synthesized in cells. They can take part in the cell activity and function efficiently when in correct subcellular location. Sequence homolog, protein-protein interaction information and traditional amino acid composition are combined as input parameters of support vector machine (SVM) to predict eukaryotic protein subcellular localization. The total accuracy of 5-fold cross validation is 91.8%, which is higher than other methods.