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

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

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Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden. lukall@u.washington.edu

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.

PMID:: 17483518; [PubMed - indexed for MEDLINE]
PMCID:: PMC1933244

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