rnafold

Quick Start

• Command: RNAfold [OPTIONS] [<input.fa>]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAfold
• Reference: See references/help.md for complete options and details

When To Use This Tool

• Predict RNA secondary structure from sequence.
• Compute minimum free energy structure and, optionally, partition-function summaries.
• Generate base-pair probability dot plots when structural uncertainty matters.
• Apply simple constraints or probing-guided folding for focused analyses.

Common Patterns

# 1) Fold a FASTA file and report MFE structures
RNAfold sequences.fa

# 2) Compute partition function and pairing probabilities
RNAfold -p sequences.fa

# 3) Suppress PostScript outputs in batch workflows
RNAfold --noPS sequences.fa

# 4) Constrained folding
RNAfold -C --enforceConstraint constrained.fa

Recommended Workflow

1. Provide RNA sequences in one-sequence-per-line or FASTA format.
2. Start with the default MFE run, then add -p if ensemble information is needed.
3. Capture stdout together with any generated plot files so sequence/structure pairs stay linked.
4. Use temperature or probing options only when the experimental context justifies them.

Guardrails

• Existing rna.ps and dot.ps-style outputs are overwritten if you reuse filenames.
• Once FASTA input is used, subsequent sequences must also be FASTA-formatted.
• -p changes the calculation and emits additional ensemble statistics and plot files.
• Use --noPS or --noDP in batch jobs that do not need PostScript artifacts.