CARNAC

CARNAC predicts conserved secondary structure elements in homologous non-coding RNA sequences without requiring prior multiple sequence alignment.

Key Features:

• Alignment-free conserved structure prediction: Predicts conserved secondary structure elements in families of homologous non-coding RNAs without prior multiple sequence alignment.
• Pairwise folding mode: Aligns a new homologous sequence with a reference structured RNA and predicts partial structures using only two input sequences.
• Local similarity and energetic modeling: Leverages local sequence similarities and stem energy considerations to identify structural elements.
• Covariation analysis: Incorporates covariation patterns to support identification of conserved base pairs.
• Low sequence similarity suitability: Effective on datasets with low primary sequence similarity.
• Demonstrated RNA classes: Applied to RNase P RNAs, ciliate telomerases, enterovirus messenger RNAs, 16S small subunit rRNA, and various viral RNAs.
• Family-level assessment: Determines whether an entire family of sequences shares common structural features.

Scientific Applications:

• Conserved structure discovery in RNA families: Identify common secondary structural elements across homologous non-coding RNA families such as RNase P and ciliate telomerases.
• Pairwise structure prediction and alignment: Predict partial structures and align a new sequence to a reference structured RNA (e.g., 16S rRNA, RNase P RNA) using two sequences.
• Viral RNA structural analysis: Analyze structural conservation in enterovirus mRNAs and various viral RNAs.

Methodology:

Uses local sequence similarities, stem energy considerations, and covariation patterns to predict conserved secondary structures and performs pairwise folding by aligning sequences with a reference while considering local similarities and structural energetics.