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Table 1 Influence of binding-affinity bias on information content. We illustrate the effect of binding-affinity bias with the given toy example of a ChIP-seq experiment for six binding sites in four species. Due to low binding-affinity, red binding sites are insufficiently bound. This results in the absence of red binding sites in the measured data which we denote binding-affinity bias. Binding sites with low binding-affinity typically comprise dissimilar bases in contrast to black binding sites with high affinity and common bases. The absence of red binding sites leads to a sharpening of the resulting motif, which we indicate using the information content. The information content without binding-affinity bias is equal in all species, whereas the information content with binding-affinity bias increases in all species. The vital point is that the effect of binding-affinity bias decreases with phylogenetic distance, which involves an increasing number of mutations. Please find a visualization of this toy example in Fig. 1 b

From: Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information