De Novo Motif Discovery

소개

This skill facilitates comprehensive sequence motif analysis, enabling researchers to uncover regulatory patterns in genomic data without prior assumptions. By leveraging the HOMER suite, it processes various inputs—including ChIP-seq peaks, ATAC-seq accessible regions, and gene lists—to detect enriched DNA sequences that may represent novel or established transcription factor binding sites. It streamlines the entire bioinformatic workflow from project initialization and genome verification to chromosome name standardization and parameter-tuned discovery, making it an essential tool for identifying potential transcriptional regulators and co-factors.

주요 기능

• Customizable analysis parameters for region size, motif length, and repeat masking
• Automated project structure initialization and standardized log management
• 2 GitHub stars
• Comprehensive motif discovery covering de novo, known, and background-corrected options
• Automatic chromosome name standardization for BED and peak file compatibility
• Support for multiple genomic formats including BED, narrowPeak, broadPeak, and gene lists

사용 사례

• Exploring uncharacterized sequence patterns in ChIP-seq or ATAC-seq data
• Analyzing promoters of a gene set to infer potential transcriptional regulators
• Identifying co-factors in TF-binding sites or differentially accessible chromatin regions