VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction

• Published in: NAR genomics and bioinformatics Vol. 7; no. 2; p. lqaf066
• Main Authors: Kirven, Kobie J, Bevilacqua, Philip C, Assmann, Sarah M
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.06.2025
• Subjects: Application Notes; Editor's Choice; Humans; Nucleic Acid Conformation; Polymorphism, Single Nucleotide; RNA - chemistry; RNA - genetics; Software
• ISSN: 2631-9268; 2631-9268
• DOI: 10.1093/nargab/lqaf066

Single nucleotide polymorphisms (SNPs) can alter RNA structure by changing the proportions of existing conformations or leading to new conformations in the structural ensemble. Such structure-changing SNPs, or riboSNitches, have been associated with diseases in humans and climate adaptation in plants. While several computational tools are available for predicting whether an SNP is a riboSNitch, these tools were generally developed to analyze individual RNAs and are not optimized for genome-wide analyses. To fill this gap, we developed VariantFoldRNA, a flexible, containerized, and automated pipeline for genome-wide prediction of riboSNitches. Our pipeline automatically installs all dependencies, can be run locally or on high-performance clusters, and is modular, enabling the user to customize the analysis for the research question of interest. VariantFoldRNA can predict riboSNitches genome-wide at user-specified temperatures and splicing conditions, opening the door to novel analyses. The pipeline is an open-source command-line tool that is freely available at https://github.com/The-Bevilacqua-Lab/variantfoldrna.