Subcellular Localisation and GPI anchor prediction in Eukaryotes

The annotation of the subcellular localization is a major step in protein functional annotation. This is particularly important in eukaryotic cells, which contain several subcellular compartments enclosed by membranes hosting different relevant functions. Methods are available for the ‘ab initio’ prediction of the subcellular localization of globular proteins, relying both on the explicit search of sorting signals in the residue sequence, or on the capture of intrinsic features coded in the aminoacidic composition. We developed BaCelLo, an SVM-based predictor that outperforms other available methods when the major localizations are discriminated: extracytoplasmic space, cytoplasm, nucleus, mitochondrion and chloroplast. A common way for targeting globular proteins to the membrane surface is the attachment with a lipid anchor. The most common and studied lipid anchor modification is the glycosylphosphatidylinositol (GPI) linkage to the C-terminal residue, upon the cleavage of a 20-30 residue long peptide. We developed GPIPE, a method based on HMMs and SVMs that is able to accurately discriminate GPI-anchored proteins in a proteome and to determine the position of the cleavage site.