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

Spencer L Nystrom,Daniel J Mckay,Mihaela Pertea

doi:10.1371/journal.pcbi.1008991

Spencer L Nystrom, Daniel J Mckay + Show 1 more

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https://doi.org/10.1371/journal.pcbi.1008991

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Abstract

Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we present memes, an R package 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 complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools, 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.

Highlights

Biopolymers, such as DNA and protein, perform varying functions based on their primary sequence
Motif analysis has become a key step in determining the function of biopolymers and in elucidating their roles in biological networks
The MEME Suite is a widely used compilation of tools used for identifying and analyzing motifs found in biological sequences

Summary

Author summary

Active molecules such as DNA, RNA, and proteins are polymers composed of repeated subunits. Motifs can serve as binding sites between molecules, they can influence the structure of molecules, and they can contribute to enzymatic activities. For these reasons, motif analysis has become a key step in determining the function of biopolymers and in elucidating their roles in biological networks. The MEME Suite is a widely used compilation of tools used for identifying and analyzing motifs found in biological sequences. J.M. from the American Cancer Society (https:// www.cancer.org/), and in part by Grant R35GM128851 to D.J.M. from the National Institute of General Medical Sciences of the NIH

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