rnaup

name	rnaup
description	Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.
disable-model-invocation	true
user-invocable	true

rnaup

Quick Start

• Command: RNAup [OPTIONS]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAup
• Reference: See references/help.md for full option details

When To Use This Tool

• Use RNAup when you need RNA-RNA interaction predictions that include site accessibility, not just duplex energy.
• It is appropriate for interaction screens where opening energy of the binding site matters, such as small RNA target accessibility analyses.
• Use -w to cap the maximum interaction length when looking for short local interactions.
• Use -b when you want unpaired-region probabilities reported for both molecules instead of the default target-focused view.

Common Patterns

# Basic accessibility-aware interaction calculation
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAup

# Increase the maximal interaction length
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAup -w 40

# Report unpaired-region probabilities for both RNAs
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAup -b

# Change the unstructured output region length
printf 'GGGAAAUCC\nGGAUUUCCC\n' | RNAup -u 8

Recommended Workflow

1. Prepare input sequences in FASTA or plain text format (T automatically converted to U unless --noconv is set)
2. Run RNAup with appropriate options (e.g., -w for max interaction length, -b for both RNAs)
3. Review output for binding energies and unpaired probabilities
4. Adjust parameters like -T for temperature or --salt for salt concentration if needed

Guardrails

• Default interaction window is 25 nucleotides; increase with -w for longer interactions
• Use -C for structure constraints only if you have reliable constraint data
• Verify energy parameters are appropriate for your organism or use -P to provide custom parameters