RNAshapes

RNAshapes analyzes RNA sequence folding landscapes using abstract shape analysis to identify multiple structurally relevant secondary structures, including pseudoknots and kissing hairpin motifs.

Key Features:

• Integration of established tools: Integrates RNAshapes, RNAalishapes, pknotsRG, pKiss, and pAliKiss to combine multiple RNA structure analysis methods.
• Pseudoknot analysis capability: Enables abstract shape analysis of structures that include pseudoknots up to the complexity of kissing hairpin motifs via pKiss.
• Prediction of kissing hairpin motifs: Predicts kissing hairpin motifs from aligned sequences using pAliKiss.
• Exploration beyond minimal free energy: Performs analysis beyond a single minimal free energy structure to explore multiple relevant configurations in the folding space.
• Extended functionality of constituent programs: Expands the functionality of the incorporated programs to provide additional analytical capabilities.

Scientific Applications:

• Analysis of complex RNA secondary structures: Study RNA sequences that form pseudoknots and kissing hairpins to assess alternative conformations and their potential functional implications.
• Comparative RNA structure analysis: Predict kissing hairpin motifs from aligned sequences for comparative studies of conserved structural features.
• Folding landscape exploration: Explore the folding space of RNA sequences to identify multiple structurally relevant conformations rather than only the minimum free energy structure.

Methodology:

Applies abstract shape analysis to map the RNA folding space and identify multiple structurally relevant configurations, integrating RNAshapes, RNAalishapes, pknotsRG, pKiss for pseudoknot handling, and pAliKiss for predicting kissing hairpin motifs from aligned sequences.