How do I install the Rnapkplex skill?

Run npx skillmds add vimalinx/rnapkplex in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Rnapkplex safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Rnapkplex?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Rnapkplex free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Rnapkplex?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Rnapkplex by vimalinx — Agent Skill

Name: Rnapkplex
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

Prepare input RNA sequence in FASTA format
Run RNAPKplex with default parameters to identify potential pseudoknots
Adjust -e (energy cutoff) or -c (probability cutoff) to filter results as needed
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

---name: rnapkplexdescription: 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.--- # 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 ```bash # 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^2*w^4) CPU time and O(n*w^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`

Frequently asked questions