RNAcop

RNAcop optimizes upstream and downstream flanking region lengths to improve constrained RNA secondary structure prediction by maximizing folding probability into a target structure.

Key Features:

• Flanking Region Optimization: Computes optimal upstream and downstream sequence lengths by evaluating probabilities of folding into a specified constrained RNA secondary structure.
• Folding Probability Impact Analysis: Quantifies how varying flanking sequence lengths influence structural stability and folding probability in known and de novo predicted RNA elements.

Scientific Applications:

• Functional RNA Element Delineation: Improves boundary definition and structural prediction of RNA functional elements within longer transcripts and supports experimental construct design.

Methodology:

RNAcop applies a probabilistic folding framework to evaluate constrained RNA secondary structures across varying flanking sequence lengths, integrating computational predictions with in vitro experimental validation.