How do I install the Rnaplex skill?

Run npx skillmds@latest add vimalinx/rnaplex 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 Rnaplex safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Rnaplex?

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 Rnaplex free to use?

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

Who published Rnaplex?

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

Rnaplex by vimalinx — Agent Skill

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

File contents

rnaplex

Quick Start

Command: RNAplex -q <query.fa> -t <target.fa>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAplex
Full reference: See references/help.md for complete options and details

When To Use This Tool

Use RNAplex when you want to scan a query RNA against a longer target and rank likely hybridization sites.
It is most appropriate for probe-like or small-RNA-like searches where only inter-molecular base pairs are modeled.
Use -a when you already have RNAplfold accessibility profiles and want accessibility-aware target scoring.
Use -p and -Q when the question is probe melting behavior rather than a generic interaction screen.

Common Patterns

# Basic query-vs-target interaction search
RNAplex -q query.fa -t target.fa

# Include precomputed accessibility profiles from RNAplfold
RNAplex -q query.fa -t target.fa -a plfold_profiles/

# Require stronger interactions and allow longer duplexes
RNAplex -q query.fa -t target.fa -l 60 -e -12

# Probe mode with explicit probe concentration
RNAplex -q query.fa -t target.fa -p -Q 0.5

Recommended Workflow

Prepare query and target RNA sequences in FASTA files
(Optional) Generate accessibility profiles using RNAplfold if incorporating accessibility effects
Run RNAplex -q <query.fa> -t <target.fa> [-a <accessibility_dir>] to compute duplex structures
Parse output: each line contains dot-bracket structure (strands separated by "&"), position ranges, and energy in kcal/mol

Guardrails

Only inter-molecular base pairs are considered; intra-molecular folding is ignored
Default maximal interaction length is 40 nt; adjust with -l for longer interactions
Accessibility profiles must be pre-computed with RNAplfold and provided via -a option

---name: rnaplexdescription: Use when screening a small query RNA against longer target RNA sequences for inter-molecular hybridization sites, especially when optional RNAplfold accessibility profiles should influence the ranking.---# rnaplex## Quick Start- **Command**: `RNAplex -q <query.fa> -t <target.fa>`- **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/RNAplex`- **Full reference**: See `references/help.md` for complete options and details## When To Use This Tool- Use `RNAplex` when you want to scan a query RNA against a longer target and rank likely hybridization sites.- It is most appropriate for probe-like or small-RNA-like searches where only inter-molecular base pairs are modeled.- Use `-a` when you already have `RNAplfold` accessibility profiles and want accessibility-aware target scoring.- Use `-p` and `-Q` when the question is probe melting behavior rather than a generic interaction screen.## Common Patterns```bash# Basic query-vs-target interaction searchRNAplex -q query.fa -t target.fa# Include precomputed accessibility profiles from RNAplfoldRNAplex -q query.fa -t target.fa -a plfold_profiles/# Require stronger interactions and allow longer duplexesRNAplex -q query.fa -t target.fa -l 60 -e -12# Probe mode with explicit probe concentrationRNAplex -q query.fa -t target.fa -p -Q 0.5```## Recommended Workflow1. Prepare query and target RNA sequences in FASTA files2. (Optional) Generate accessibility profiles using RNAplfold if incorporating accessibility effects3. Run `RNAplex -q <query.fa> -t <target.fa> [-a <accessibility_dir>]` to compute duplex structures4. Parse output: each line contains dot-bracket structure (strands separated by "&"), position ranges, and energy in kcal/mol## Guardrails- Only inter-molecular base pairs are considered; intra-molecular folding is ignored- Default maximal interaction length is 40 nt; adjust with `-l` for longer interactions- Accessibility profiles must be pre-computed with RNAplfold and provided via `-a` option

Frequently asked questions

Rnaplex