MARZ: an algorithm to combinatorially analyze gapped n -mer models of transcription factor binding (BMC Bioinformatics)

Background: A key challenge in understanding the molecular mechanisms that control gene regulation is the characterization of the specificity with which transcription factor proteins bind to specific DNA sequences. A number of computational approaches have been developed to examine these interactions, including simple mononucleotide and dinucleotide position weight matrix models. Results: Here we develop a novel, unbiased computational algorithm, MARZ, that systematically analyzes all possible gapped matrices across a fixed number of nucleotides. In addition, to evaluate the ability of these matrix models to predict in vivo binding sites, we utilize a new scoring system and, in combination with established scoring methods and statistical analysis, test the performance of 32 different gapped matrices on the well characterized HUNCHBACK transcription factor in Drosophila. Conclusions: Our results indicate that in many cases gapped matrix models can outperform traditional models, but that the relative strength of the binding sites considered in the analysis can profoundly influence the predictive ability of specific models.