Pscan

Pscan scans sets of DNA sequences (e.g., promoters from co-expressed or co-regulated genes) using transcription factor binding motifs to identify and assess motifs that are significantly over- or under-represented and to detect candidate transcription factor binding sites.

Key Features:

• Motif scanning: Scans input DNA sequences with motifs that describe the binding specificity of known transcription factors to locate candidate binding sites.
• Motif enrichment analysis: Assesses which motifs are significantly over- or under-represented within the provided sequence set.
• Empirical performance: Reported comparisons indicate reduced false positive predictions and optimized computation time relative to similar methods.

Scientific Applications:

• Gene expression studies: Identification of common transcription factor motifs among co-expressed genes to infer shared regulators.
• Functional genomics: Mapping predicted transcription factor binding sites to elucidate regulatory roles of transcription factors across genomic contexts.
• Comparative genomics support: Identification of conserved regulatory motifs that can complement comparative analyses despite not relying on orthologous sequence comparisons.

Methodology:

Pscan performs motif-based scanning of input DNA sequences and statistically evaluates motif over- or under-representation, operating without comparisons to orthologous sequences.