Modeling dependencies between positions in protein-DNA binding motifs

State-of-the-art methods for identifying and modeling the motifs mediating protein-DNA binding use Position Weight Matrices as a model for the motif, implicitely assuming the statistical independence of the nucleotides within the motif. Dropping this hypothesis is a two-fold challenge: the structure of these dependencies has to be inferred from the available data, whose limited amount also imposes a parsimony requirement on the model. After an introduction to this field of bioinformatics, the statistical underpinnings of a solution proposed jointly with Ivo Grosse (University of Halle) will be presented.