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

Abstract

Sequence logos have been a prominent visualization tool in biological research since their inception two decadesago. Their primary use is in communicating conservation of biological sequences (protein, DNA or RNA), toindicate 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, beingselected against, reveal a loss of fitness for living organism or cells. Criticism of the sequence logo has longexisted, 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 thereported flaws of the sequence logo. In addition to our improvements, we propose glyph based enhancements, tohighlight qualitatively relevant chemical insights resulting from residue substitution between sequences