VariantFoldRNA

VariantFoldRNA predicts single nucleotide polymorphisms (SNPs) that alter RNA structure (riboSNitches) transcriptome-wide or genome-wide.

Key Features:

• Genome-wide riboSNitch prediction: Predicts riboSNitches at user-specified temperatures and splicing conditions.
• Containerized and automated dependency installation: Automatically installs all dependencies via containerization.
• Flexible execution: Can be run locally or on high-performance clusters.
• Modular architecture: Enables customization of the analysis for specific research questions.

Scientific Applications:

• Disease association research: Identifies riboSNitches associated with human diseases.
• Climate adaptation studies: Identifies riboSNitches involved in climate adaptation in plants.
• Transcriptome-wide structural analysis: Analyzes RNA structural changes across the transcriptome or genome.

Methodology:

VariantFoldRNA is implemented as a Snakemake pipeline.