lamm-mit/skills/jaspar-database

JASPAR Database Skill - Complete Content

Name: jaspar-database

Description: "Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulatory genomics, motif analysis, and GWAS regulatory variant interpretation."

License: CC0-1.0

Skill Author: Kuan-lin Huang

Overview

JASPAR (https://jaspar.elixir.no/) serves as the authoritative open-access repository of curated transcription factor binding profiles represented as position frequency matrices. The 2024 version contains approximately 1,210 non-redundant profiles across 164 eukaryotic species, with each profile derived from experimental validation methods.

Core Capabilities

The skill provides REST API access and Python implementations for:

1. Profile searching by transcription factor name, species, family, or classification
2. Matrix retrieval with PFM/PWM conversion and scoring
3. Sequence scanning across forward and reverse complement strands
4. Variant impact assessment comparing reference versus alternative allele binding affinity
5. Multi-TF workflow automation for promoter and regulatory element analysis

Key Workflows

• Finding all binding sites in promoter regions
• Assessing regulatory variant effects on transcription factor recognition
• Motif enrichment analysis from ChIP-seq and ATAC-seq data

Best Practices

The resource recommends using the CORE collection for most analyses, setting thresholds at 80% of maximum score for general prediction, always scanning both DNA strands, and validating predictions against experimental ChIP-seq datasets.