RNAsnp

RNAsnp detects local changes in RNA secondary structure induced by single nucleotide polymorphisms (SNPs) to assess their potential impact on noncoding RNAs and mRNA cis-regulatory elements.

Key Features:

• Local Structural Change Detection: Identifies local regions where structural differences between mutant and wild-type RNA sequences are maximal.
• Screening Mode for Genome-Wide Applications: Employs a screening mode that approximates local regions with maximal structural discrepancies for large-scale analyses.
• Quantification of Mutation Effects: Quantifies structural effects of mutations using empirical P values.
• Precomputed Tables for Efficiency: Uses extensive precomputed tables mapping SNP effects as functions of RNA length and GC content to accelerate analysis and reduce reliance on shuffling-based approaches.
• Application to Disease-Associated SNPs: Validated on 501 human-inherited disease-associated SNPs, predicting 54 SNPs with significant local structural effects in untranslated regions (UTRs) of mRNAs.

Scientific Applications:

• Functional Genomics: Pinpoints SNPs that cause significant local RNA structural changes to inform functional interpretation of genetic variants.
• Disease Research: Identifies disease-associated SNPs with structural impacts relevant to studies of inherited disorders.
• RNA Biology: Provides insights into how local structural variation influences RNA stability, interactions, and regulatory functions.

Methodology:

Compares mutant and wild-type secondary structures to locate local maxima of structural change; uses a screening mode to approximate local regions for genome-wide analyses; quantifies significance with empirical P values; and leverages precomputed tables indexed by RNA length and GC content to avoid shuffling-based approaches.