PCRTiler

PCRTiler generates tiled PCR primer pairs to comprehensively cover large genomic regions and enable specific PCR amplification for applications such as ChIP and genomic scanning.

Key Features:

• Automated Tiling Design: Automates design of tiled primer pairs to cover extensive genomic loci.
• Integration with Primer3 and BLAST: Uses Primer3 to identify candidate primers and BLAST to filter primers with high cross-hybridization potential.
• User-Specified Parameters: Allows customization of tiling density and primer characteristics to match experimental requirements.

Scientific Applications:

• ChIP experiments: Produces primer sets for comprehensive mapping of protein–DNA interactions across large genomic regions.
• Empirical validation on human genome: In a test region, 96 of 123 primer pairs amplified on first attempt and an additional 9 pairs were recovered after optimization, yielding an overall 85% success rate.

Methodology:

Target sequences are divided into sub-regions; Primer3 identifies candidate primers for each sub-region; candidate primers undergo BLAST analysis to remove those with high cross-hybridization potential.