jaspar-motifs skillA
jaspar-motifs is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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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. …
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How to install
mdr add ammawla/encode-toolkit/jaspar-motifs@git:20260312.665e731mdr add ammawla/encode-toolkit/jaspar-motifs@sha256:00675d79d196e301Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
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