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Nucleic Acids Research Advance Access published online on May 8, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp363
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© 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

TOPCONS: consensus prediction of membrane protein topology

Andreas Bernsel, Håkan Viklund, Aron Hennerdal and Arne Elofsson*

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Sweden

*To whom correspondence should be addressed. Tel: +46 8 164276; Fax: +46 8 153679; Email: arne{at}bioinfo.se The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received December 13, 2008. Revised April 22, 2009. Accepted April 22, 2009.

TOPCONS (http://topcons.net/) is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by ~10 percentage points. The web interface allows for constraining parts of the sequence to a known inside/outside location, and detailed results are displayed both graphically and in text format.


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