rnapvmin

name	rnapvmin
description	Use when working with RNA soft constraints and need to compute pairing probabilities with position-specific perturbation minimization from the ViennaRNA package.
disable-model-invocation	true
user-invocable	true

rnapvmin

Quick Start

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

When To Use This Tool

• Infer a perturbation vector that reconciles predicted pairing probabilities with experimental SHAPE-derived probabilities.
• Generate soft-constraint inputs for downstream ViennaRNA folding runs.
• Optimize per-position perturbations instead of hard-coding one SHAPE transformation.
• Study how strongly experimental probing data must bias the folding model.

Common Patterns

# 1) Compute a perturbation vector from a sequence on stdin plus a SHAPE file
echo 'GGGAAAUCC' | RNApvmin observations.shape > perturbation.txt

# 2) Choose a specific SHAPE-to-probability conversion model
echo 'GGGAAAUCC' | RNApvmin --shapeConversion=O observations.shape > perturbation.txt

# 3) Tune the optimization with more samples and a custom tau/sigma ratio
echo 'GGGAAAUCC' | RNApvmin --sampleSize=1000 --tauSigmaRatio=1.0 observations.shape > perturbation.txt

Recommended Workflow

1. Prepare your RNA sequence input in the appropriate format
2. Run RNApvmin with required options (see references/help.md for available parameters)
3. Capture the output pairing probabilities or constraint data
4. Use the output as soft constraints in downstream RNA structure prediction tools

Guardrails

• In this environment the binary currently fails to start because libopenblas.so.0 is missing, so live help/version output is unavailable until that dependency is fixed.
• The sequence is read from stdin, while the positional argument is a SHAPE file whose lines must look like [position] [nucleotide] [absolute_shape_reactivity].
• Use conservative language when documenting this tool: some option details here come from binary strings rather than successful runtime help.