Computational tools for protein-DNA interactions

Interactions between deoxyribonucleic acid (DNA) and proteins are central to living systems, and characterizing how and when they occur would greatly enhance our understanding of working genomes. We review the computational problems associated with protein-DNA interactions and the various methods used to solve them. A wide range of topics is covered including physics-based models for direct and indirect recognition, identification of transcription-factor-binding sites, and methods to predict DNA-binding proteins. Our goal is to introduce this important problem domain to data mining researchers by identifying the key issues and challenges inherent to the area as well as provide directions for fruitful future research. (C) 2011 Wiley Periodicals, Inc.