rMSA

Key Features:

• Hierarchical Homolog Search and Alignment: Applies a hierarchical pipeline for sensitive homolog detection and accurate alignment tailored to target RNA sequences.
• Automated High-Quality MSA Generation: Produces optimized MSAs that improve RNA secondary structure prediction accuracy and increase F1-scores for long-range contact prediction compared to RNAcmap.

Scientific Applications:

• RNA Structure Modeling: Enhances prediction of RNA secondary structures and long-range contacts for functional and structural analysis.

Methodology:

rMSA performs iterative, hierarchical homolog searches followed by refined multiple sequence alignment to construct high-quality MSAs that support downstream RNA secondary structure and contact prediction.