DepLogo: visualizing sequence dependencies in R

Abstract

Summary: Statistical dependencies are present in a variety of sequence data, but are not discernible from traditional sequence logos. Here, we present the R package DepLogo for visualizing inter-position dependencies in aligned sequence data as dependency logos. Dependency logos make dependency structures, which correspond to regular co-occurrences of symbols at dependent positions, visually perceptible. To this end, sequences are partitioned based on their symbols at highly dependent positions as measured by mutual information, and each partition obtains its own visual representation. We illustrate the utility of the DepLogo package in several use cases generating dependency logos from DNA, RNA and protein sequences.

Availability and implementation: The DepLogo R package is available from CRAN and its source code is available at https://github.com/Jstacs/DepLogo.

Supplementary information: Supplementary data are available at Bioinformatics online.