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Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal.
(Lelieveld et al., 2015) ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites. Nucleic acids research.