Memes: A motif analysis environment in R using tools from the MEME Suite

摘要

Identification of biopolymer motifs represents a key step in the analysis of biologicalsequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopoly mer motifs; however, these tools are poorly integrated within popular analysis frameworkslike the R/Bioconductor project, creating barriers to their use. Here we present memes, an Rpackage that provides a seamless R interface to a selection of popular MEME Suite tools.memes provides a novel “data aware” interface to these tools, enabling rapid and complexdiscriminative motif analysis workflows. In addition to interfacing with popular MEME Suitetools, memes leverages existing R/Bioconductor data structures to store the multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally,memes provides data visualization capabilities to facilitate communication of results.memes is available as a Bioconductor package at https://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.