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

Nucleic acids research, 2007-07, Vol.35 (Web Server issue), p.W429-W432 [Peer Reviewed Journal]

2007 The Author(s) 2007 ;ISSN: 0305-1048 ;ISSN: 1362-4962 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkm256 ;PMID: 17483518

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Title:
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
Author: Käll, Lukas ; Krogh, Anders ; Sonnhammer, Erik L.L
Subjects: Computational Biology - methods ; Computer Simulation ; Cytoplasm - metabolism ; Internet ; Medicin och hälsovetenskap ; Membrane Proteins - metabolism ; Models, Molecular ; Models, Theoretical ; Programming Languages ; Protein Conformation ; Protein Sorting Signals - physiology ; Protein Structure, Secondary - physiology ; Proteomics - methods ; Software
Is Part Of: Nucleic acids research, 2007-07, Vol.35 (Web Server issue), p.W429-W432
Description: 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.
Publisher: England: Oxford University Press
Language: English
Identifier: ISSN: 0305-1048
ISSN: 1362-4962
EISSN: 1362-4962
DOI: 10.1093/nar/gkm256
PMID: 17483518
Source: Oxford Journals Open Access Collection
DOAJ Directory of Open Access Journals
GFMER Free Medical Journals
MEDLINE
PubMed Central
Alma/SFX Local Collection
SWEPUB Freely available online

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

2007 The Author(s) 2007 ;ISSN: 0305-1048 ;ISSN: 1362-4962 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkm256 ;PMID: 17483518

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