A Brief History of Sequence Logos

Abstract

For nearly three decades, sequence logo plots have served as the standard tool for graphical representation of aligned DNA, RNA and protein sequences. Over the years, a large number of packages and web applications have been developed for generating these logo plots and using them to identify conserved patterns in sequences called motifs. Also, over time, we have seen a considerable upgrade in the look, flexibility of data handling and the overall scope of these plots in biological applications and beyond. Here I attempt to review some popular tools for generating sequence logos, with a focus on how these plots have evolved over time since their origin and how I view the future for these plots.

dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data

“…To facilitate the discovery of conserved patterns from increasingly accumulated proteomic data, we developed the dagLogo package, which have been well downloaded and cited by researchers [4,80,91,92]. Though it does not provide a graphic user interface as other web applications for sequence logo generators (See S1 Table), our package helps to identify and visualize differentially used AA residues or AA residue groups in given protein sequences, improving and extending the sophisticated logo generator iceLogo.…”

“…Since their first introduction in 1990, sequence logos have been widely used to visualize conserved patterns among large sets of nucleic acid and peptide sequences [1][2][3][4]. Dozens of sequence logo generators with different functionalities and performances have been developed; these generators require various types of inputs and background models, and use different algorithms and graphical representations [1][2][3][5][6][7][8][9][10][11][12][13][14][15].…”

dagLogo: an R/Bioconductor Package for Identifying and Visualizing Differential Amino Acid Group Usage in Proteomics data

“…Since their first introduction in 1990, sequence logos have been widely used to visualize conserved patterns among large sets of nucleic acid and peptide sequences [1][2][3][4]. Dozens of sequence logo generators with different functionalities and performances have been developed; these generators require various types of inputs and background models, and use different algorithms and graphical representations [1][2][3][5][6][7][8][9][10][11][12][13][14][15].…”