PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties
| Autor: | Bart Hooghe, Pieter De Bleser, Stefan Broos, Arne Soete, Frans van Roy, Raymond J. Moran |
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| Rok vydání: | 2013 |
| Předmět: |
In silico
PROTEIN-DNA RECOGNITION Computational biology Biology DNA-binding protein Transcription (biology) Genetics ELEMENTS Humans A-DNA Binding site Promoter Regions Genetic Transcription factor Gene Telomerase Internet Binding Sites Biology and Life Sciences DNA Sequence Analysis DNA Articles GENE DNA binding site DNA-Binding Proteins UCSC GENOME BROWSER Algorithms Software Transcription Factors |
| Zdroj: | Nucleic Acids Research NUCLEIC ACIDS RESEARCH |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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