title: Modeling protein-DNA binding via high-throughput in vitro technologies.
abstract: Protein-DNA binding plays a central role in gene regulation and by that in all processes in the living cell. Novel experimental and computational approaches facilitate better understanding of protein-DNA binding preferences via high-throughput measurement of protein binding to a large number of DNA sequences and inference of binding models from them. Here we review the state of the art in measuring protein-DNA binding in vitro, emphasizing the advantages and limitations of different technologies. In addition, we describe models for representing protein-DNA binding preferences and key computational approaches to learn those from high-throughput data. Using large experimental data sets, we test the performance of different models based on different measuring techniques. We conclude with pertinent open problems.
authors: Yaron
authors: Y
authors: Orenstein
authors: Ron
authors: R
authors: Shamir
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA
keywords: high-throughput SELEX; motif finding; protein-binding microarrays; protein–DNA binding