SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

Abstract

Abstract Summary: SPOCTOPUS is a method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies. Its objective is to minimize false predictions of transmembrane regions as signal peptides and vice versa. We provide a description of the SPOCTOPUS algorithm together with a performance evaluation where SPOCTOPUS compares favorably with state-of-the-art methods for signal peptide and topology predictions. Availability: SPOCTOPUS is available as a web server and both the source code and benchmark data are available for download at http://octopus.cbr.su.se/ Contact: arne@bioinfo.se Supplementary information: Supplementary data are available at Bioinformatics online.

Keywords

Benchmark (surveying)Computer scienceSource codeTopology (electrical circuits)Signal peptideSIGNAL (programming language)Transmembrane proteinCode (set theory)Web serverData miningMembrane topologyDownloadTheoretical computer scienceComputational biologyAlgorithmArtificial intelligenceBiologyThe InternetMathematicsPeptide sequenceGeneGeneticsWorld Wide Web

MeSH Terms

AlgorithmsEscherichia coliGenomeBacterialGenomeFungalMembrane ProteinsNeural NetworksComputerProtein Sorting SignalsSaccharomyces cerevisiaeSequence AnalysisProteinSoftware

Affiliated Institutions

Stockholm University SE

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Publication Info

Year: 2008
Type: article
Volume: 24
Issue: 24
Pages: 2928-2929
Citations: 238
Access: Closed

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APA Style

                            
                                
                                    Håkan Viklund, 
                                
                                    Andreas Bernsel, 
                                
                                    Marcin J. Skwark
                                
                                et al.
                            
                            (2008). 
                            SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. 
                            Bioinformatics
                            , 24
                            (24)
                            , 2928-2929.
                            https://doi.org/10.1093/bioinformatics/btn550
                        

Identifiers

DOI: 10.1093/bioinformatics/btn550
PMID: 18945683

Data Quality

Data completeness: 86%