The presence of signal peptide significantly affects transmembrane topology prediction

In summary, the presence of signal peptide in the TM sequence has significantly influenced prediction performance of the ten selected TM topology prediction methods. Unlike in signal peptide, the presence of transit peptide in the TM sequence has not significantly affected the prediction performance of the ten selected TM topology prediction methods. In addition, higher prediction accuracy can be expected if the signal peptide is removed either before or after prediction analysis. Regarding the question on which of the two signal peptide treatment is appropriate-removed first or later-the choice depends on the TM topology prediction method used, although statistically, the gain in prediction accuracy is the same. Furthermore, it is imperative that when performing genome wide analyses of TM protein topology, the issue on signal peptide presence should be properly addressed. This study also has demonstrated that signal peptide should be removed if present, which can be done either before or after prediction analysis. Although, at this point, it is still premature to assert strongly as regards the effect of signal peptide on TM topology prediction until more experimentally characterized topology data of TM proteins with signal peptide are available for evaluation.