Predicting peroxisomal proteins

PTS1 proteins are peroxisomal matrix proteins that have a well conserved targeting motif at the C-terminal end. However, this motif is present in many non peroxisomal proteins as well, thus predicting peroxisomal proteins involves differentiating fake PTS1 signals from actual ones. In this paper we report on the development of an SVM classifier with a separately trained logistic output function. The model uses an input window containing 12 consecutive residues at the C-terminus and the amino acid composition of the full sequence. The final model gives a Matthews Correlation Coefficient of 0.77, representing an increase of 54% compared with the well-known PeroxiP predictor. We test the model by applying it to several proteomes of eukaryotes for which there is no evidence of a peroxisome, producing a false positive rate of 0.088%.