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Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
Open accessAbstract
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.
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Metadata
- Authors
- Kall, L., Krogh, A., & Sonnhammer, E. L. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-08
- Volume
- 35
- Issue
- Web Server
- Pages
- W429-W432
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2124088653
- Cited by
- 1,677
- References
- 0
- FWCI
- 14.37
- Type
- journal article
- Language
- en
- Open access
- gold
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