Journal
BRIEFINGS IN FUNCTIONAL GENOMICS
Volume 16, Issue 3, Pages 171-180Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bfgp/elw030
Keywords
motif finding; protein-DNA binding; protein-binding microarrays; high-throughput SELEX
Funding
- Israel Science Foundation [317/13]
- Israeli Center of Research Excellence (I-CORE), Gene Regulation in Complex Human Disease [41/11]
- Raymond and Beverly Sackler Chair in Bioinformatics
- Edmond J. Safra Center for Bioinformatics at Tel Aviv University
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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.
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