rnaaliduplex

name	rnaaliduplex
description	Use when predicting conserved RNA-RNA interactions between two CLUSTAL alignments to identify evolutionary conserved binding sites, hybridization energies, and duplex structures.
disable-model-invocation	true
user-invocable	true

rnaaliduplex

Quick Start

• Command: RNAaliduplex [options] <file1.aln> <file2.aln>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAaliduplex
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Predict conserved RNA-RNA interactions between two homologous alignments.
• Score duplexes while preserving evolutionary signal across matched sequence sets.
• Search for optimal and suboptimal binding sites between a probe alignment and a target alignment.
• Keep analysis focused on inter-molecular pairing only.

Common Patterns

# 1) Predict the best conserved interaction between two alignments
RNAaliduplex probe.aln target.aln

# 2) Report suboptimal interactions within an energy band
RNAaliduplex -e 5 probe.aln target.aln

# 3) Sort reported interactions by energy
RNAaliduplex -e 10 -s probe.aln target.aln > duplexes.txt

Recommended Workflow

1. Prepare two CLUSTAL format alignment files with equal numbers of sequences in matching order
2. Run RNAaliduplex <file1.aln> <file2.aln> to compute conserved duplex structures
3. Use -e <range> to explore suboptimal structures within an energy range of the optimum (kcal/mol)
4. Parse stdout output containing dot-bracket structures with "&" separator, position ranges, and energies in kcal/mol

Guardrails

• Both input alignments must have equal numbers of sequences in identical order (1st sequence in file1 pairs with 1st in file2)
• Only inter-molecular base pairs are calculated; for general folding use RNAcofold
• Output is written to stdout; redirect to file to capture results