Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it���s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

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

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Lao DM, Arai M, Ikeda M, Shimizu T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics. 2002;18:1562–1566. - PubMed
    1. Klee EW, Ellis LBM. Evaluating eukaryotic secreted protein prediction. BMC Bioinformatics. 2005;6:256. - PMC - PubMed
    1. Käll L, Krogh A, Sonnhammer ELL. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 2004;338:1027–1036. - PubMed
    1. Krogh A, Larsson B, vonHeijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001;305:567–580. - PubMed
    1. Nielsen H, Engelbrecht J, Brunak S, vonHeijne G. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst. 1997;8:581–599. - PubMed

Publication types