TrawlerWeb

TrawlerWeb performs de novo motif discovery and predicts transcription factor binding site (TFBS) composition from DNA sequences derived from next-generation sequencing (NGS) experiments.

Key Features:

• De novo motif discovery: Performs de novo motif discovery on input DNA sequences.
• TFBS composition prediction: Predicts transcription factor binding site (TFBS) composition for identified motifs.
• NGS input (BED): Accepts BED files generated from NGS experiments as input.
• Input-matched biological background: Automatically generates input-matched biological background sequences for enrichment analysis.
• Conservation scores: Reports conservation scores for each identified motif instance to aid prioritization.
• Performance: Provides a fast motif-discovery implementation suitable for large NGS-derived datasets.

Scientific Applications:

• Transcriptional regulation analysis: Identify enriched motifs and predict TFBS composition to study gene regulation mechanisms.
• Regulatory element discovery: Detect novel cis-regulatory elements in non-coding genomic regions from NGS data.
• Experimental prioritization: Prioritize motif instances for experimental validation using reported conservation scores.

Methodology:

Performs de novo motif discovery on DNA sequences (BED input from NGS), generates an input-matched biological background, identifies enriched motifs, assigns conservation scores to motif instances, and predicts TFBS composition.