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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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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.
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.
Chicago author-date
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.
Chicago author-date (all authors)
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.
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.
IEEE
[1]
S. Broos, A. Soete, B. Hooghe, R. Moran, F. Van Roy, and P. De Bleser, “PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties,” NUCLEIC ACIDS RESEARCH, vol. 41, no. W1, pp. W531–W534, 2013.
@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 >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}},
  keywords     = {{GENE,ELEMENTS,PROTEIN-DNA RECOGNITION,UCSC GENOME BROWSER}},
  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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