Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server
2007 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, no Web Server issue, 1, W429-W432 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2007. Vol. 35, no Web Server issue, 1, W429-W432 p.
Bioinformatics (Computational Biology)
IdentifiersURN: urn:nbn:se:kth:diva-48861DOI: 10.1093/nar/gkm256ISI: 000255311500081PubMedID: 17483518OAI: oai:DiVA.org:kth-48861DiVA: diva2:458736
QC 201506242011-11-232011-11-232015-06-23Bibliographically approved