Journal
NUCLEIC ACIDS RESEARCH
Volume 41, Issue W1, Pages W531-W534Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt288
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Funding
- Agency for Innovation through Science and Technology in Flanders [091213]
- Research Foundation - Flanders (FWO) [G.0235.10]
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium
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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.
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