rnapkplex

name	rnapkplex
description	Use when searching an RNA sequence for pseudoknot-forming interactions by combining local accessibility with interaction energy, especially when ordinary pseudoknot-free folding is insufficient.
disable-model-invocation	true
user-invocable	true

rnapkplex

Quick Start

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

When To Use This Tool

• Use RNAPKplex when pseudoknots are central to the structural hypothesis and pseudoknot-free RNA folding tools are not sufficient.
• It is useful for flagging putative pseudoknot sites by combining local accessibility with interaction energy gain.
• Use the probability cutoff -c to suppress weakly accessible candidate sites and -e to demand stronger pseudoknot stabilization.
• Use -s when you want near-optimal pseudoknot alternatives instead of only the best one.

Common Patterns

# Basic pseudoknot search from stdin
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex

# Require stronger energy gain before reporting pseudoknots
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -e -10

# Filter low-accessibility candidate regions
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -c 1e-4

# Include near-optimal suboptimal pseudoknot solutions
printf '>seq\nGGGAAAUCCCUUU\n' | RNAPKplex -s 2

Recommended Workflow

1. Prepare input RNA sequence in FASTA format
2. Run RNAPKplex with default parameters to identify potential pseudoknots
3. Adjust -e (energy cutoff) or -c (probability cutoff) to filter results as needed
4. Use -s to explore suboptimal structures within a specified energy range

Guardrails

• Algorithm uses O(n^2w^4) CPU time and O(nw^2) memory; avoid very long sequences
• Always uses dangle=2 model; this cannot be configured
• Default energy cutoff is -8.10 kcal/mol; pseudoknots with less favorable energy gains are rejected
• The skill name is rnapkplex, but the actual executable is capitalized as RNAPKplex