rnacofold

name	rnacofold
description	Use when predicting secondary structures of two RNA sequences with dimerization, computing equilibrium concentrations of monomer and dimer species, or analyzing RNA-RNA hybridization thermodynamics.
disable-model-invocation	true
user-invocable	true

rnacofold

Quick Start

• Command: RNAcofold [OPTIONS] < input.txt
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAcofold
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Fold two RNAs together as a heterodimer or homodimer candidate.
• Compare MFE-only duplexes with ensemble-aware predictions using -p.
• Compute monomer/dimer free energies for concentration-dependent analyses.
• Estimate equilibrium concentrations for A, B, AA, BB, and AB species.

Common Patterns

# 1) Fold one RNA pair as a dimer candidate
echo 'AUGCUA&UAGCAU' | RNAcofold

# 2) Add partition function and pairing probabilities
echo 'AUGCUA&UAGCAU' | RNAcofold -p

# 3) Compute all species and equilibrium concentrations
RNAcofold -a -c -f concentrations.txt < pairs.fa

Recommended Workflow

1. Prepare input sequences concatenated with & as separator (e.g., AUGCU&GCAUA)
2. Run RNAcofold -p to compute MFE structure plus partition function and pairing probabilities
3. Use -a -c options to compute free energies and equilibrium concentrations for all species
4. Review bracket notation output and PostScript structure plots for dimerization analysis

Guardrails

• Sequences must be concatenated with & character as separator; otherwise dimerization is not computed
• Equilibrium concentration calculations require the -c flag and initial monomer concentrations
• Use -T to rescale energy parameters when analyzing at non-physiological temperatures (default 37°C)