e-RNA

e-RNA provides computational methods for comparative RNA secondary structure prediction, detection of conserved and transient helices including pseudo-knots, co-transcriptional folding-aware minimum-free energy (MFE) prediction, and structure visualization to support evolutionary and functional analysis of RNA sequences.

Key Features:

• Transat: Detects conserved helices from multiple sequence alignments, including transient, alternative, and pseudo-knotted helices.
• RNA-Decoder: Uses evolutionary models to identify conserved RNA secondary structures within alignments that are partly protein-coding.
• SimulFold: Simultaneously estimates conserved (potentially pseudo-knotted) structures, alignments, and phylogenetic trees from homologous input sequences.
• CoFold: Predicts minimum-free energy (MFE) structures while incorporating co-transcriptional folding dynamics to improve accuracy for long RNA sequences.
• R-chie: Visualizes RNA secondary structures as arc diagrams for comparison of conserved base-pairs and quantitative structural features.

Scientific Applications:

• Comparative genomics: Detects and compares conserved RNA structural elements across multiple sequence alignments.
• Evolutionary biology: Integrates structure prediction with phylogenetic analysis to study conservation and evolution of RNA structures.
• Functional genomics: Identifies conserved secondary structures within coding and noncoding regions to inform functional annotation.
• RNA folding dynamics: Models transient helices and co-transcriptional folding effects to investigate RNA folding pathways.

Methodology:

Transat and RNA-Decoder analyze multiple sequence alignments to detect conserved structural elements; SimulFold simultaneously estimates structures (including potential pseudo-knots), alignments, and phylogenetic trees; CoFold predicts MFE structures incorporating co-transcriptional folding dynamics.