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PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties

Stefan Broos (UGent) , Arne Soete (UGent) , Bart Hooghe (UGent) , Raymond Moran, Frans Van Roy (UGent) and Pieter De Bleser (UGent)
(2013) NUCLEIC ACIDS RESEARCH. 41(W1). p.W531-W534
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Abstract
The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php.
Keywords
GENE, ELEMENTS, PROTEIN-DNA RECOGNITION, UCSC GENOME BROWSER

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Chicago
Broos, Stefan, Arne Soete, Bart Hooghe, Raymond Moran, Frans Van Roy, and Pieter De Bleser. 2013. “PhysBinder : Improving the Prediction of Transcription Factor Binding Sites by Flexible Inclusion of Biophysical Properties.” Nucleic Acids Research 41 (W1): W531–W534.
APA
Broos, S., Soete, A., Hooghe, B., Moran, R., Van Roy, F., & De Bleser, P. (2013). PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. NUCLEIC ACIDS RESEARCH, 41(W1), W531–W534.
Vancouver
1.
Broos S, Soete A, Hooghe B, Moran R, Van Roy F, De Bleser P. PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. NUCLEIC ACIDS RESEARCH. 2013;41(W1):W531–W534.
MLA
Broos, Stefan, Arne Soete, Bart Hooghe, et al. “PhysBinder : Improving the Prediction of Transcription Factor Binding Sites by Flexible Inclusion of Biophysical Properties.” NUCLEIC ACIDS RESEARCH 41.W1 (2013): W531–W534. Print.
@article{4144011,
  abstract     = {The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from {\textrangle}60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php.},
  author       = {Broos, Stefan and Soete, Arne and Hooghe, Bart and Moran, Raymond and Van Roy, Frans and De Bleser, Pieter},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  language     = {eng},
  number       = {W1},
  pages        = {W531--W534},
  title        = {PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties},
  url          = {http://dx.doi.org/10.1093/nar/gkt288},
  volume       = {41},
  year         = {2013},
}

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