PromPredict

PromPredict predicts promoter regions in genomic DNA by detecting local decreases in DNA duplex stability that mark transcription start site (TSS)-associated promoters.

Key Features:

• Promoter identification: Identifies promoter regions within genomic DNA sequences, focusing on non-coding regulatory regions associated with transcription initiation.
• DNA duplex stability analysis: Compares stability between putative promoter regions and their flanking genomic sequences to locate destabilized regions.
• Average free energy calculation: Quantifies local instability through variations in average free energy across the sequence.
• GC-content correlation: Correlates average free energy values with the GC content of the flanking genomic sequence to adjust predictions.
• Threshold-based classification: Uses GC-dependent free energy threshold values as a generic criterion to predict promoter locations.

Scientific Applications:

• Microbial promoter prediction (Escherichia coli): Predicted promoters corresponding to experimentally validated TSSs in Escherichia coli (50.8% GC) with 99% sensitivity and 58% precision.
• Microbial promoter prediction (Bacillus subtilis): Predicted promoters corresponding to experimentally validated TSSs in Bacillus subtilis (43.5% GC) with 95% sensitivity and 60% precision.
• Microbial promoter prediction (Mycobacterium tuberculosis): Predicted promoters corresponding to experimentally validated TSSs in Mycobacterium tuberculosis (65.6% GC) with 100% sensitivity and 49% precision.

Methodology:

Analyze stability differences between promoter regions and neighboring sequences by computing average free energy, correlate free energy with GC content, and apply GC-dependent free energy threshold values to classify promoter locations.