Redesigning the Sequence Logo with Glyph-based Approaches to Aid Interpretation

Figure 1: A) A ‘traditional’ sequence logo from [Bio13] showing: top the consensus across 1809 protein sequences; middle gram negative bacteria; and bottom gram positive bacteria. B) Our sequence logo visualizing the same data as in A. This approach keeps in place the idea of the original sequence logo but removes the dominance of letters for space filling and adds glyphs to visualize overall properties of the dominating amino acids at a sequence location (e.g. charge and hydropathy). Abstract Sequence logos have been a prominent visualization tool in biological research since their inception two decades ago. Their primary use is in communicating conservation of biological sequences (protein, DNA or RNA), to indicate largest conservation at particular positions namely places where only ever one or two possible residues (nucleotides or amino acids) are observed. Conservation is indicative of functional importance, as changes, being selected against, reveal a loss of fitness for living organism or cells. Criticism of the sequence logo has long existed, largely directed towards perception problems caused through use of letter height to indicate frequency. Here, we present a solution for use as a static image in publications or interactively on the web to address the reported flaws of the sequence logo. In addition to our improvements, we propose glyph based enhancements, to highlight qualitatively relevant chemical insights resulting from residue substitution between sequences.