Fig. 3
From: Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Intra-motif dependencies and multiple motif occurrences. The two sequence logos of the left show the motif inferred by a PMM1 for the CTCF and CHD2 data sets. After applying a mixture model of two PWM components on the underlying predicted binding sites, we obtain a clustering that can be represented by two sequence logos. For CTCF, we observe that both sequence logos are similar and resemble the original prediction, and differences among both logos are just an alternative representation of the dependencies at the 3’ end of the motif. For CHD2, we observe that both sequence logos are fundamentally different at all positions. Hence, the corresponding binding sites appear to be bound by two different proteins and just co-occur within the same ChIP-seq data set