Find transcription factor binding motifs

Validate TF binding targets and discover co-factors using PWM motif scanning

Confirming ChIP-seq specificity or discovering co-binding regulatory complexes when gold-standard target validation is required.

• · ENCODE ChIP-seq peak coordinates
• · JASPAR motif ID (e.g., MA0139.1)

• · Motif enrichment results
• · Co-binding TF predictions
• · Validated binding sites with sequence specificity

• · ENCODE/UCSC genomics APIs
• · Database
• · HTTP/REST API
• · LLM/Claude API

• · JASPAR REST API access (no auth required)
• · Peak coordinates in BED format
• · GRCh38 or appropriate assembly

• · PWM specificity varies by TF class (zinc fingers vs forkheads)
• · Low-complexity sequences cause false positives
• · Peak calling quality affects motif discovery

• · JASPAR curated profiles (900+ TFs)
• · FIMO gold-standard tool integration
• · Cites canonical ENCODE validation studies