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Bioinformatics Advance Access originally published online on October 22, 2008
Bioinformatics 2008 24(24):2928-2929; doi:10.1093/bioinformatics/btn550
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Håkan Viklund , Andreas Bernsel , Marcin Skwark and Arne Elofsson *

Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University SE-10691 Stockholm, Sweden

*To whom correspondence should be addressed.


  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{at}bioinfo.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on June 19, 2008; revised on October 20, 2008; accepted on October 21, 2008

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