RT Journal Article
SR Electronic
T1 A new sequence logo plot to highlight enrichment and depletion
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 226597
DO 10.1101/226597
A1 Kushal K. Dey
A1 Dongyue Xie
A1 Matthew Stephens
YR 2017
UL http://biorxiv.org/content/early/2017/11/29/226597.abstract
AB Background Sequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos.Results We introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles.Conclusion Our new EDLogo plots, and flexible software implementation, can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc) across a wide range of applications.