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

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W429-32. doi: 10.1093/nar/gkm256. Epub 2007 May 5.


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. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface ( and to access Phobius.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Computer Simulation
  • Cytoplasm / metabolism
  • Internet
  • Membrane Proteins / metabolism*
  • Models, Molecular*
  • Models, Theoretical
  • Programming Languages
  • Protein Conformation
  • Protein Sorting Signals / physiology*
  • Protein Structure, Secondary / physiology*
  • Proteomics / methods
  • Software


  • Membrane Proteins
  • Protein Sorting Signals