rnamultifold

name	rnamultifold
description	Use when predicting secondary structures and base pairing probabilities for multiple interacting RNA molecules
disable-model-invocation	true
user-invocable	true

rnamultifold

Quick Start

• Command: RNAmultifold [OPTION]... [FILE]...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAmultifold
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Fold more than two interacting RNA strands in one complex.
• Compare one chosen multimer arrangement with the ensemble of all possible complexes.
• Add partition-function probabilities to multi-strand MFE predictions.
• Estimate concentrations for all species formed from the supplied strands.

Common Patterns

# 1) Fold a specific multi-strand arrangement
echo 'AUGCUA&UAGCAU&GGAUCC' | RNAmultifold

# 2) Add partition function and pair probabilities
echo 'AUGCUA&UAGCAU&GGAUCC' | RNAmultifold -p

# 3) Compute all complexes and concentration estimates
RNAmultifold -a -c -f concentrations.txt < complexes.fa

Recommended Workflow

1. Prepare input sequences with multiple strands concatenated using '&' as separator (e.g., SEQUENCE_A&SEQUENCE_B)
2. Run RNAmultifold with appropriate flags: -p for partition function, -a for all complexes up to the input count
3. Review the PostScript dot plot output file for base pairing probabilities
4. Use -c or --concfile to compute equilibrium concentrations if needed

Guardrails

• Multiple strands must be concatenated with the '&' character as separator; sequences are read one per line
• Temperature defaults to 37°C; use -T to adjust energy parameters for non-standard conditions
• Terminate batch input with a single @ character on its own line or EOF signal