DeFCoM

'DeFCoM' is a software tool that has been developed to identify the locations of transcription factor binding sites within genome-wide data produced by DNase-seq and ATAC-seq experiments. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct 'footprint' patterns at binding sites. The identification of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions.
The tool is a supervised learning footprinter that models the heterogeneity in the data by introducing a novel approach to detect footprints containing motifs. A large degree of previously uncharacterized site-to-site variability exists in footprint signals across motif sites for a transcription factor, and almost all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites. DeFCoM overcomes this limitation and outperforms current methods in determining bound and unbound motif sites.