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Bioinformatics Advance Access published online on October 22, 2008
Bioinformatics, 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

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

1Department 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. Dr. Arne Elofsson, E-mail: arne{at}bioinfo.se


  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 avorably 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

Associate Editor: Prof. Burkhard Rost

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

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