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Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-5689-9797
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
Abstract [en]

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 ( and to access Phobius.

Place, publisher, year, edition, pages
2007. Vol. 35, no Web Server issue, 1, W429-W432 p.
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-48861DOI: 10.1093/nar/gkm256ISI: 000255311500081PubMedID: 17483518OAI: diva2:458736

QC 20150624

Available from: 2011-11-23 Created: 2011-11-23 Last updated: 2015-06-23Bibliographically approved

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Käll, Lukas
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Gene TechnologySeRC - Swedish e-Science Research CentreScience for Life Laboratory, SciLifeLab
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