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Last pushed: 2 years ago
Short Description
Ubuntu 14.10 with GraphProt v.1.1.1
Full Description

This Image contains "GraphProt: modeling binding preferences of RNA-binding proteins" Version v.1.1.1.

Tools installed

  • libsvm
  • gnuplot
  • python (linux default)
  • R: installed the r-base version (R version 3.0.2)
  • R plyr: installed
  • R stats: installed
  • weblogo: installed version 3.2
  • numpy: installed
  • perf: installed

Keywords:
iCLIP, PAR-CLIP, ..

Maticzka et al. Genome Biology 2014, 15:R17
http://genomebiology.com/2014/15/1/R17

Abstract Info:
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.

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Owner
tschwarzl

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