universalmotif: An R package for biological motif analysis

Abstract

Sequence motifs are an important concept in molecular biology, as specific repeating patterns in DNA, RNA and proteins form the basis of biological regulation. Identifying and characterizing these motifs is therefore a important part of studying various aspects of cellular processes, such as gene regulation, transcript stability, and protein function. Many programs have been developed over the years to tackle these tasks, though their interoperability remains poor. The universalmotif package has two main goals: to serve as a go-between for most common biological motif programs and Bioconductor packages used by the research community, and to provide a robust set of tools for basic motif analysis and manipulation in R. Tools for motif and sequence manipulation, scanning, enrichment, comparison, shuffling and P-value computation are included.