How do I install the Rnasnoop skill?

Run npx skillmds add vimalinx/rnasnoop 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 Rnasnoop 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 Rnasnoop?

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 Rnasnoop free to use?

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

Who published Rnasnoop?

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

Rnasnoop by vimalinx — Agent Skill

Name: Rnasnoop
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

rnasnoop

Quick Start

Command: RNAsnoop -s <query_file> -t <target_file>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAsnoop
Full reference: See references/help.md for complete options and details

When To Use This Tool

Use RNAsnoop when the biological question is specifically about H/ACA snoRNA target prediction, not general RNA-RNA duplexing.
It is tailored to snoRNA-target geometry and stem constraints, so it is more appropriate than generic ViennaRNA interaction tools for this niche case.
Use -P or -U when accessibility profiles from RNAplfold or RNAup should be incorporated into target ranking.
Reach for the duplex/stem-length filters when your snoRNA architecture differs from the defaults or you need to tighten candidate selection.

Common Patterns

# Basic H/ACA snoRNA target search
RNAsnoop -s sno.fa -t target.fa

# Add accessibility profiles from RNAplfold
RNAsnoop -s sno.fa -t target.fa -P plfold_profiles/

# Add accessibility profiles from RNAup
RNAsnoop -s sno.fa -t target.fa -U rnaup_profiles/

# Tighten stem-length and energy filters for stricter candidate selection
RNAsnoop -s sno.fa -t target.fa -h 6 -i 80 -q -1200

Recommended Workflow

Prepare query file containing the H/ACA snoRNA sequence and target file containing the RNA sequence to search
Run RNAsnoop -s <query.fa> -t <target.fa> to compute hybridization structures
Review output: dot-bracket structures with <> for snoRNA intramolecular interactions and () for intermolecular duplexes, including energy values in kcal/mol
Optionally provide accessibility profiles via -P (RNAplfold) or -U (RNAup) to improve target prediction accuracy

Guardrails

This tool is specialized for H/ACA snoRNA target prediction only; for general RNA-RNA interactions use RNAduplex, RNAup, RNAcofold, or RNAplex instead
Energy threshold options expect values in decacal/mol (not kcal/mol); a threshold of -2.8 kcal/mol should be specified as -280
Default parameter values assume typical H/ACA snoRNA stem lengths (5-120 nt) and duplex-box distances (11-16 nt); adjust -h/-i and -j/-k if your snoRNA differs significantly
RNAsnoop -h does not show help; -h is the minimal stem length option, so use --help for usage text

---name: rnasnoopdescription: Use when searching target RNAs for interactions with a query H/ACA snoRNA, especially when the search should respect H/ACA-specific structural constraints and optionally use accessibility profiles.--- # rnasnoop ## Quick Start - **Command:** `RNAsnoop -s <query_file> -t <target_file>` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/RNAsnoop` - **Full reference:** See [references/help.md](references/help.md) for complete options and details ## When To Use This Tool - Use `RNAsnoop` when the biological question is specifically about **H/ACA snoRNA target prediction**, not general RNA-RNA duplexing. - It is tailored to snoRNA-target geometry and stem constraints, so it is more appropriate than generic ViennaRNA interaction tools for this niche case. - Use `-P` or `-U` when accessibility profiles from `RNAplfold` or `RNAup` should be incorporated into target ranking. - Reach for the duplex/stem-length filters when your snoRNA architecture differs from the defaults or you need to tighten candidate selection. ## Common Patterns ```bash # Basic H/ACA snoRNA target search RNAsnoop -s sno.fa -t target.fa # Add accessibility profiles from RNAplfold RNAsnoop -s sno.fa -t target.fa -P plfold_profiles/ # Add accessibility profiles from RNAup RNAsnoop -s sno.fa -t target.fa -U rnaup_profiles/ # Tighten stem-length and energy filters for stricter candidate selection RNAsnoop -s sno.fa -t target.fa -h 6 -i 80 -q -1200 ``` ## Recommended Workflow 1. Prepare query file containing the H/ACA snoRNA sequence and target file containing the RNA sequence to search 2. Run `RNAsnoop -s <query.fa> -t <target.fa>` to compute hybridization structures 3. Review output: dot-bracket structures with `<>` for snoRNA intramolecular interactions and `()` for intermolecular duplexes, including energy values in kcal/mol 4. Optionally provide accessibility profiles via `-P` (RNAplfold) or `-U` (RNAup) to improve target prediction accuracy ## Guardrails - This tool is specialized for H/ACA snoRNA target prediction only; for general RNA-RNA interactions use RNAduplex, RNAup, RNAcofold, or RNAplex instead - Energy threshold options expect values in decacal/mol (not kcal/mol); a threshold of -2.8 kcal/mol should be specified as -280 - Default parameter values assume typical H/ACA snoRNA stem lengths (5-120 nt) and duplex-box distances (11-16 nt); adjust `-h/-i` and `-j/-k` if your snoRNA differs significantly - `RNAsnoop -h` does not show help; `-h` is the minimal stem length option, so use `--help` for usage text

Frequently asked questions