ProSampler

ProSampler discovers transcription factor (TF) binding motifs and cooperative motifs from large ChIP-seq datasets to support mapping of cis-regulatory elements.

Key Features:

• Ultra-Fast Performance: Operates significantly faster than existing motif-finding tools, achieving orders-of-magnitude speed improvements for large ChIP-seq datasets.
• High Accuracy: Employs a novel numeration technique combined with the Gibbs sampling algorithm to accurately identify motifs associated with target TFs and their cooperative partners.
• Combinatory Motif Discovery: Detects cooperative interactions among multiple transcription factors in addition to individual TF binding sites.
• Implementation: Implemented in C++ and compatible with Linux, macOS, and Windows.

Scientific Applications:

• Motif discovery in ChIP-seq: Identification of TF binding sites and cooperative motifs from ChIP-seq datasets.
• Regulatory element mapping: Mapping cis-regulatory elements and TF interactions to study transcriptional regulation.
• Genomics and systems biology: Supporting analyses in genomics, epigenetics, and systems biology that require comprehensive motif identification.

Methodology:

Combines a novel numeration technique with Gibbs sampling to perform motif discovery on large ChIP-seq datasets.