Bioinformatics Advance Access originally published online on April 21, 2008
Bioinformatics 2008 24(11):1325-1331; doi:10.1093/bioinformatics/btn198
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Eukaryotic transcription factor binding sites—modeling and integrative search methods
Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA
*To whom correspondence should be addressed.
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Abstract |
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A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. Current state-of-the-art techniques for improving computational identification of binding sites can be broadly categorized into two classes: (1) approaches that aim to improve binding motif models by extracting maximal sequence information from experimentally determined binding sites and (2) approaches that supplement binding motif models with additional genomic or other attributes (such as evolutionary conservation). In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development.
Contact: sridharh{at}pcbi.upenn.edu
Associate Editor: Jonathan Wren
Received on February 11, 2008; revised on April 18, 2008; accepted on April 18, 2008
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