Description of the CCTOP server
Signal peptide prediction
Predicting signal peptides before the topology prediction is also an important and sometimes neglected tool, as most topology predictions were reported to suffer from misprediction of signal peptides due to the similar physical-chemical properties of signal peptides and transmembrane helices (TMHs). All transit peptides have been cleaved (if BLAST finds the identical entry in UniProt), then the signal peptides have been predicted by SignalP. This prediction was modified if a homologous protein in the TOPDB database had an annotated signal peptide that was not predicted by SignalP, or vice versa, if the corresponding TOPDB entry had not contained a signal peptide, but it was predicted by SignalP.