THiCweed: fast, sensitive detection of sequence features by clustering big datasets.We present THiCweed, a new approach to analyzing transcription factor binding data from high-throughput chromatin immunoprecipitation-sequencing (ChIP-seq) experiments.  THiCweed clusters bound regions based on sequence similarity using a divisive hierarchical clustering approach based on sequence similarity within sliding windows, while exploring both strands.  ThiCweed is specially geared toward data containing mixtures of motifs, which present a challenge to traditional motif-finders.  THiCweed performs best with large 'window' sizes (≥50 bp), much longer than typical binding sites (7-15 bp).  THiCweed thus goes beyond traditional motif finding to give new insights into genomic transcription factor-binding complexity.
THiCweed