Known Motif Scanning

About

Automate the detection of specific transcription factor (TF) binding motifs within experimental genomic data to gain deeper insights into regulatory biology. This skill leverages HOMER to scan genomic regions for precise motif locations using position-specific scoring matrices, offering capabilities to search genome-wide, target specific peaks, or annotate existing datasets. It handles complex pre-processing tasks like chromosome name standardization and motif format conversion, providing researchers with standardized BED and TXT outputs for seamless integration into visualization tools and downstream analysis pipelines.

Key Features

• Supports multiple input formats including BED, narrowPeak, broadPeak, and HOMER peak files
• 2 GitHub stars
• Generates motif-annotated BED files ready for genome browser visualization and feature analysis
• Provides automated chromosome name standardization and motif format conversion from MEME to HOMER
• Executes comprehensive motif scanning using HOMER for high-precision binding site detection
• Offers specialized modes for region-specific scanning, genome-wide searching, and peak annotation

Use Cases

• Identifying co-factor motif co-occurrence to infer cooperative binding mechanisms
• Evaluating motif distribution patterns relative to transcription start sites or enhancers
• Validating TF binding specificity within ChIP-seq or ATAC-seq peak regions