DiffLogo: a comparative visualization of sequence motifs

Abstract

BackgroundFor three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain.ResultsHere, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form. Here, the motifs are ordered by similarity, and the difference logos are colored for clarity. We demonstrate the benefit of DiffLogo on CTCF motifs from different human cell lines, on E-box motifs of three basic helix-loop-helix transcription factors as examples for comparison of DNA motifs, and on F-box domains from three different families as example for comparison of protein motifs.Conclusions DiffLogo provides an intuitive visualization of motif differences. It enables the illustration and investigation of differences between highly similar motifs such as binding patterns of transcription factors for different cell types, treatments, and algorithmic approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0767-x) contains supplementary material, which is available to authorized users.

A Massively Parallel Selection of Small Molecule-RNA Motif Binding Partners Informs Design of an Antiviral from Sequence

“…32 By comparing the LOGOS for related compounds, or DiffLogos, 33 structure-activity relationships (SARs) can be defined. Indeed, various hit compounds differ by a single functional group, including compounds 1 and 2 (Figure 5).…”

“…“Enriched” and “discriminated” sequences were kept separate using JMP, Version 13.2.1 (SAS Institute, Cary, NC). The R package Difflogo, 33 which is part of Bioconductor, was utilized to create the sequence logos from PWM lists for each compound and visually compare the differences between them.…”

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

“…The resulting matrices were plotted using DiffLogo. 77 Prediction of piRNA clusters and loci from sequencing data piRNA cluster detection was performed on Nematostella piRNAs using the proTRAC pipeline version 2.1 78 with the options protrac_nv (Supplemental Table S3) for each developmental stage. Clusters were then merged using the bedtools suite, 79 resulting in 457 clusters.…”

METTL4 catalyzes m6Am methylation inU2 snRNAto regulate pre-mRNA splicing

“…The Jensen-Shannon Divergences of splice site sequence subsets and associated tests for statistical significance were calculated using DiffLogo (60). All other sequence logos were generated using ggseqlogo (61).…”