motif-scanning

What problem does it solve?

Identifies exact locations of known transcription factor motifs within experimental genomic regions such as ChIP-seq or ATAC-seq peaks, enabling interpretation of regulatory elements.

Core Features & Use Cases

• HOMER-based motif scanning: Uses position-specific scoring matrices from known motif databases to detect occurrences of transcription factor motifs within input regions.
• Flexible inputs: Accepts peak formats like BED, narrowPeak, broadPeak, or HOMER peak files and supports genome assemblies such as hg38, mm10, hg19, or mm9.
• Output and downstream analysis: Produces motif-hit lists and optional BED/annotation outputs, enabling downstream visualization and co-factor motif analysis.

Quick Start

Provide your peak file and genome assembly to run HOMER motif scanning and save results.