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Open Access Method

GraphProt: modeling binding preferences of RNA-binding proteins

Daniel Maticzka1, Sita J Lange1, Fabrizio Costa1 and Rolf Backofen12*

Author Affiliations

1 Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany

2 Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany

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Genome Biology 2014, 15:R17  doi:10.1186/gb-2014-15-1-r17

Published: 22 January 2014

Abstract

We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt webcite.