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

TY - JOUR

T1 - Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.

AU - Käll, Lukas

AU - Krogh, Anders

AU - Sonnhammer, Erik L L

N1 - Keywords: Computational Biology; Computer Simulation; Cytoplasm; Internet; Membrane Proteins; Models, Molecular; Models, Theoretical; Programming Languages; Protein Conformation; Protein Sorting Signals; Protein Structure, Secondary; Proteomics; Software

PY - 2007

Y1 - 2007

N2 - 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. Udgivelsesdato: 2007-Jul

AB - 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. Udgivelsesdato: 2007-Jul

U2 - 10.1093/nar/gkm256

DO - 10.1093/nar/gkm256

M3 - Journal article

C2 - 17483518

SN - 0305-1048

VL - 35

SP - W429-32

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Web Server issue

ER -