jaspar-motifs SKILL.md skillA
jaspar-motifs from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/jaspar-motifs@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
skills/jaspar-motifs/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 23,863 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Using JASPAR Transcription Factor Binding Profiles with ENCODE ChIP-seq Data Integrate JASPAR position weight matrices (PWMs) with ENCODE ChIP-seq peaks to validate TF binding targets, discover co-binding partners, and scan regulatory elements for TF binding potential. ## Scientific Rationale **The question**: "Does the expected TF binding motif appear in my ENCODE ChIP-seq peaks, and what other TF motifs are enriched?" ENCODE TF ChIP-seq experiments identify where a transcription factor binds in the genome, but the peak coordinates alone do not confirm direct DNA binding or reveal the binding sequence specificity. JASPAR provides curated position weight matrices (PWMs) — mathematical representations of TF binding preferences — that enable two critical analyses: 1. **Target validation**: If CTCF ChIP-seq peaks are enriched for the CTCF motif (JASPAR MA0139.1), the experiment worked correctly. If they are NOT enriched, something may be wrong with the antibody, crosslinking, or peak calling. 2. **Co-factor discovery**: Motif enrichment analysis in ChIP-seq peaks often reveals motifs for co-binding TFs that were not the ChIP target, uncovering regulatory complexes. …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/jaspar-motifs@sha256:e7a4119247decaf4The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_su6w5uakgjwocxjw)
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Versions
The registry has recorded 4 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 65 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 23,863 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 22,621 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 22,640 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 22,651 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (23863 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
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- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_su6w5uakgjwocxjw GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/jaspar-motifs GET https://markdownregistry.com/api/v1/blob/e7a4119247decaf478f65fc35d3466b5a54be414fad9c2bc26433ecdead17d92
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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