RNAz

RNAz predicts functional RNA secondary structures in multiple sequence alignments by integrating thermodynamic stability and structural conservation.

Key Features:

• Structure conservation measurement: Computes a consensus secondary structure from aligned RNA sequences to detect conserved structural elements.
• Thermodynamic stability assessment: Calculates a normalized thermodynamic stability metric akin to a z-score, adjusted for sequence length and base composition, and does not require sampling from shuffled sequences.
• High sensitivity and specificity: Demonstrates high sensitivity and specificity in detecting functional RNA secondary structures, outperforming previous methods in accuracy and speed.
• Scalability: Applicable to large-scale genomic screens and analysis of extensive genomic regions.

Scientific Applications:

• Genomic screening: Applied to screen all alignments longer than 50 nucleotides in the Comparative Regulatory Genomics database, identifying known noncoding RNAs and cis-acting elements with high significance.
• Discovery of novel structures: Provided evidence for numerous conserved RNA secondary structures not previously documented.
• Evolutionary conservation analysis: Combines sequence covariation and thermodynamic stability to achieve over 80% prediction reliability for related sequences, as demonstrated in studies involving rRNAs and Early Noduline mRNA.

Methodology:

Computes a consensus secondary structure from multiple sequence alignments and calculates a normalized thermodynamic stability metric (z-score–like) adjusted for sequence length and base composition without relying on shuffled-sequence sampling.