TPpred3 is a web-server ot detect and discriminate mitochondrial and chloroplastic targeting peptides in eukaryotic proteins

Molecular recognition of N-terminal targeting peptides is the most common mechan- ism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can annotate targeting peptides, and determine their cleavage sites for characterizing protein localization, function, and mature protein sequences. The problem of discriminating mitochondrial from chloroplastic propeptides is particularly relevant when annotating proteomes of photosynthetic Eukaryotes, endowed with both types of sequences. Here, we introduce TPpred3, a computational method that given any Eukaryotic protein sequence performs three different tasks: (i) the detection of targeting peptides; (ii) their classifica- tion as mitochondrial or chloroplastic and (iii) the precise localization of the cleavage sites in an organelle-specific framework. Our implementation is based on our TPpred previously introduced. Here, we integrate a new N-to-1 Extreme Learning Machine specifically designed for the classifica- tion task (ii). For the last task, we introduce an organelle-specific Support Vector Machine that exploits sequence motifs retrieved with an extensive motif-discovery analysis of a large set of mito- chondrial and chloroplastic proteins. We show that TPpred3 outperforms the state-of-the-art meth- ods in all the three tasks.