Mfold

Mfold predicts the secondary structure of single-stranded nucleic acids (RNA and DNA) and provides folding and hybridization analyses.

Key Features:

• Structure plots: Generates structure plots for predicted secondary structures with optional reliability information.
• Single-strand frequency plots: Computes single-strand frequency plots for individual sequences.
• Energy dot plots: Produces energy dot plots for individual sequence folding.
• Visualization outputs: Provides comprehensive outputs to visualize and interpret predicted secondary structures.
• Bulk processing: Supports bulk processing of up to hundreds of sequences with faster turnaround and reduced per-sequence detail.
• Pseudoknot handling: Does not predict pseudoknots and directs pseudoknot prediction to the PKNOTS tool.

Scientific Applications:

• Secondary structure analysis: Interpreting RNA and DNA secondary structure for studies of nucleic acid structure and function.
• Hybridization analysis: Analyzing folding and hybridization behavior of single-stranded nucleic acids.
• High-throughput folding: Performing high-throughput folding analyses across hundreds of sequences.
• Pseudoknot-specific workflows: Incorporating PKNOTS for workflows that require pseudoknot prediction.

Methodology:

Performs computational secondary-structure prediction for individual sequences and generates structure plots, single-strand frequency plots, and energy dot plots, with optional bulk processing that reduces per-sequence output detail.