motif-analysis

motif-analysis is a skill for Claude Code from ammawla/encode-toolkit. It costs 104 tokens per session (5,752 once invoked), scanned A, original, AGPL-3.0.

A guide to motif analysis, the search for short DNA patterns that may be recognized by transcription factors, which are proteins that regulate genes. It covers finding new patterns and checking known ones in DNA peaks from ChIP-seq or ATAC-seq.

In plain words
What is it for?
Use it to discover likely transcription-factor binding motifs, check whether known targets are supported, and look for factors that may bind together.
Why use it?
It helps interpret a list of DNA peaks instead of leaving them as unexplained genomic coordinates. It also brings together the HOMER and MEME Suite tools for pattern enrichment analysis.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the encode-toolkit plugin — 47 skills, 1 MCP server shipped together

Good fit Use it to discover likely transcription-factor binding motifs, check whether known targets are supported, and look for factors that may bind together.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/ammawla/encode-toolkit/motif-analysis
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add ammawla/encode-toolkit --skill motif-analysis
Clone the repo
git clone --depth 1 https://github.com/ammawla/encode-toolkit

Made for: Claude Code.

Or install encode-toolkit, the plugin that ships this one along with the rest of its 47 skills, 1 MCP server.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for motif-analysis

README.md
[![agentmods](https://agentmods.dev/badge/skills/ammawla/encode-toolkit/motif-analysis/github.svg)](https://agentmods.dev/skills/ammawla/encode-toolkit/motif-analysis)
Your own site
<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/motif-analysis"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/motif-analysis/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for motif-analysis

Your own site · 80×15
<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/motif-analysis"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/motif-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 104 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 5,752 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00104 $0.05752
Opus 5.5 $0.00042 $0.02301
Sonnet 5.5 $0.00021 $0.01150
Haiku 4.5 $0.00010 $0.00575

Measured 1mo ago against content hash 097bd1b13578, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

motif-analysis scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

wget https://jaspar.elixir.no/download/data/2024/CORE/JASPAR2024_CORE_vertebrates_non-redundant_pfms_meme.txt \
plugin/skills/motif-analysis/SKILL.md · 489 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago Changed · +12 lines 097bd1b13578
  2. 1mo ago First seen · 477 lines · 104 tokens per session scan A f87d901a748e

Subscribe to this mod's changes

motif-analysis is a skill published in the GitHub repository ammawla/encode-toolkit (21 stars, last pushed 26d ago), licensed AGPL-3.0. It adds 104 tokens to every session and 5,752 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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