PETfold and PETcofold

PETfold and PETcofold predict conserved RNA secondary structures and RNA interactions by combining probabilistic evolutionary models with thermodynamic stability to identify conserved structural motifs across multiple sequence alignments.

Key Features:

• Probabilistic evolutionary and thermodynamic models: Integration of probabilistic models of sequence evolution with thermodynamic folding principles to predict RNA secondary structures and interaction sites.
• Integration with annotated RNA alignments: Direct use of annotated alignments including resources such as the Rfam 10.0 database for contextualizing predictions within known RNA families.
• Comparative genomics alignments: Support for multiple alignments from 16 vertebrate genomes with human to enable cross-species conservation analysis of RNA structures.

Scientific Applications:

• Non-coding RNA research: Prediction of secondary structures and interaction sites to inform studies of non-coding RNA function.
• Biological role and pathway inference: Structural predictions used to generate hypotheses about RNA-mediated biological roles and pathways.
• Gene regulation, disease mechanisms, and evolutionary studies: Comparative structural analysis to investigate regulatory mechanisms, molecular bases of disease, and evolutionary conservation.

Methodology:

Analysis of multiple RNA sequences to identify conserved structural motifs and interaction sites using probabilistic models that account for sequence evolution together with thermodynamic models that enforce energetic feasibility.