Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server

Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer

Abstract: When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30–65% of all predicted signal peptides and 25–35% of all predicted transmembrane topologies overlap. This impairs predictions of 5–10% of the proteome, hence this is an important issue in protein annotation.