Predicting signal peptides with support vector machines

Abstract

We examine using a Support Vector Machine to predict secretory signal peptides. We predict signal peptides for both prokaryotic and eukaryotic signal organisms. Signalling peptides versus non-signaling peptides as well as cleavage sites were predicted from a sequence of amino acids. Two types of kernels (each corresponding to different metrics) were used: hamming distance, a distance based upon the percent accepted mutation (PAM) score trained on the same signal peptide data.