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Fig. 2 | BMC Bioinformatics

Fig. 2

From: A new sequence logo plot to highlight enrichment and depletion

Fig. 2

Comparison of standard logo plot, weighted KL (w-KL) logo plot and EDLogo plot on four examples. Panel (a): the transcription factor binding site of the EBF1-disc1 transcription factor from the ENCODE project [14]. Panel (b): The N-linked glycosylation motif, with the site of the N amino acid at the center (position 0), and 5 bases on either side of the N (based on data from UniprotKB [19]). The EDLogo clearly shows the N-X- S/T motif where X represents any amino acid except proline (P). Panel (c): a somatic mutation signature (signature 12 from [20]). The heights of the strings in the center of each plot (C→G, C→T, etc at position 0 on x axis) reflect the relative frequency of each substitution type among somatic mutations contributing to the signature, while the heights of the bases at flanking positions (-2,-1,1,2 on x axis) reflect the relative frequency of each base at positions flanking these somatic mutations. The depletion of G at position +1 - possibly occurring due to the rarity of CpG sites owing to de-amination of methylated cytosines - is clearest in the EDLogo plot. Panel (d): relative abundance of histone modification sites across various genomic regions in the lymphoblastoid cell line GM06990 (Table S2 in Koch et al. 2007 [10]). These examples illustrate the ability of the EDLogo plot to highlight both enrichment and depletion, while avoiding unnecessarily visual clutter. The last two examples also illustrate how our software allows arbitrary strings as elements in a logo plot

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