Rnaduplex

rnaduplex

Quick Start

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

When To Use This Tool

• Use RNAduplex when you want the hybridization structure between two RNA strands and only care about inter-molecular base pairs.
• It is especially suited to probe-target style questions, such as a short RNA or oligo against a longer target.
• Use -e when you need near-optimal alternative duplexes, not just the best-scoring interaction.
• Do not use it as a general cofolding tool when each strand may also form substantial intra-molecular structure; that is outside its simplified model.

Common Patterns

# Predict the best duplex for two sequences from stdin
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAduplex

# Enumerate suboptimal duplexes within 2 kcal/mol of the optimum
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAduplex -e 2

# Sort reported duplexes by free energy
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAduplex -e 2 -s

# Recalculate hybridization under a different temperature
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAduplex -T 25

Recommended Workflow

1. Prepare two RNA sequences as input (stdin or file), noting that "T" is auto-converted to "U" unless --noconv is set
2. Run RNAduplex with relevant options (e.g., -s to sort by free energy, -e <range> for suboptimal structures within an energy range)
3. Parse the output: dot-bracket structure with & separating strands, position ranges (from,to : from,to), and energy in kcal/mol
4. Adjust model parameters if needed (e.g., -T for temperature, --salt for salt concentration, -P for custom energy parameters)

Guardrails

• For general cases requiring intra-molecular base pairs, use RNAcofold instead
• Default temperature is 37°C and salt concentration is 1.021M; adjust for non-physiological conditions
• Only inter-molecular base pairs are considered; this tool is optimized for probe-target scenarios