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

Area of Science:

• Genomics
• Computational Biology
• RNA Biology

Background:

• Single nucleotide polymorphisms (SNPs) can alter RNA structure and function.
• Structure-changing SNPs, termed riboSNitches, are linked to human diseases and plant adaptation.
• Existing computational tools are not optimized for genome-wide riboSNitch prediction.

Purpose of the Study:

• To develop an automated, flexible, and containerized pipeline for genome-wide riboSNitch prediction.
• To provide a tool optimized for large-scale analysis of RNA structure-altering SNPs.

Main Methods:

• Developed VariantFoldRNA, a command-line pipeline for automated riboSNitch prediction.
• The pipeline supports local or high-performance cluster execution and allows user customization.
• It can predict riboSNitches genome-wide under user-specified temperatures and splicing conditions.

Main Results:

• VariantFoldRNA facilitates genome-wide prediction of riboSNitches.
• The pipeline automates dependency installation and is modular for customized analyses.
• Enables novel analyses of riboSNitches across genomes.

Conclusions:

• VariantFoldRNA addresses the need for efficient, genome-wide riboSNitch prediction.
• The tool supports flexible analysis conditions, enhancing RNA structure variation studies.
• Provides an open-source solution for researchers studying the impact of SNPs on RNA structure.