Correlated evolution of positions within mammalian cis elements.

Abstract excerpt

Transcriptional regulation critically depends on proper interactions between transcription factors (TF) and their cognate DNA binding sites. The widely used model of TF-DNA binding--the positional weight matrix (PWM)--presumes independence between positions within the binding site. However, there is evidence to show that the independence assumption may not always hold, and the extent of interposition dependence...

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