Program for Identification of sub-cellular localization of Eukaryotic proteins: Plants

Protcomp-PL combines several methods of protein localization prediction - neural networks-based prediction; direct comparison with updated base of homologous proteins of known localization; comparisons of pentamer distributions calculated for query and DB sequences; prediction of certain functional peptide sequences, such as signal peptides, signal-anchors, GPI-anchors, transit peptides of mitochondria and chloroplasts and transmembrane segments; and search for certain localization-specific motifs. It means that the program treats correctly complete sequences only, containing signal sequences, anchors, and other functional peptides, if any. The program includes separately trained recognizers for animal/fungal and plant proteins, which dramatically improves recognition accuracy. The following table provides approximate prediction accuracy for each compartment of animal/fungal proteins. Testing was performed on a samples of proteins of known localization (~200 in each localization), which were NOT included in training samples for the programs.