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

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

Lukas Käll  1 , Anders Krogh, Erik L L Sonnhammer
Affiliations

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

Lukas Käll et al. Nucleic Acids Res. 2007 Jul.

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. 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 (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.

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Figures

Figure 1.
Figure 1.
The Phobius model. The model comprise submodels for signal peptides, transmembrane helices, cytoplasmic loops and two different submodels for non-cytoplasmic loops.
Figure 2.
Figure 2.
Output from the Phobius web server. An optional posterior probability plot is included in the prediction result.
See this image and copyright information in PMC

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