PhysBinder: Improving the Prediction of Transcription Factor Binding Sites by Flexible Inclusion of Biophysical Properties

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Apr 27

PMID 23620286

Citations 20

Authors

Stefan Broos

Arne Soete

Bart Hooghe

Raymond Moran

Frans van Roy

Pieter De Bleser

Affiliations

Soon will be listed here.

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.

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