RNAalishapes

RNAalishapes predicts RNA secondary structures using abstract shape analysis to enumerate multiple relevant conformations within the folding space rather than a single minimal free energy structure.

Key Features:

• Abstract Shape Analysis: Extracts and classifies structural configurations into predefined abstract shape classes to represent conformational diversity.
• Integration with RNAshapes, pknotsRG, and pKiss: Combines established algorithms to support secondary structure prediction, including pseudoknots up to kissing hairpin complexity.
• pAliKiss Module: Predicts kissing hairpin motifs directly from aligned RNA sequences.

Scientific Applications:

• RNA Structural Dynamics Analysis: Identifies alternative secondary structures and complex pseudoknot motifs in regulatory and viral RNAs using multiple sequence alignments.

Methodology:

RNAalishapes analyzes RNA multiple sequence alignments, abstracts predicted structures into shape classes, and integrates RNAshapes, pknotsRG, pKiss, and pAliKiss to model secondary structures including pseudoknots and kissing hairpin motifs beyond minimal free energy constraints.