primerdiffer

primerdiffer designs PCR primers to enable scalable, specific primer selection for haplotype differentiation and genotyping of hybrid/introgression strains.

Key Features:

• Batch primer design: Supports batch processing of primer design tasks for genome-wide screening projects.
• Haplotype differentiation: Designs primers to distinguish haplotypes and enable analysis of genetic variation, including genotyping of Caenorhabditis briggsae and Caenorhabditis nigoni introgression strains.
• False priming checking: Integrates local and global in silico PCR-based checks to detect potential false priming and improve primer specificity.
• Greedy primer search and automated selection: Uses a greedy search to enumerate candidate primers across target regions and automatically selects primer sets based on predefined specificity and efficiency criteria.
• Flexible, user-defined parameters: Accepts user-provided genome sequences and supports customization of design constraints and filtering thresholds.
• Experimental validation: Validated by single-worm PCR using species-specific primers for genotyping hybrid introgression strains.

Scientific Applications:

• Haplotype differentiation and genotyping: Enables discrimination of haplotypes and genotyping of hybrid/introgression strains such as Caenorhabditis briggsae and Caenorhabditis nigoni.
• Genome-wide screening: Supports scalable primer design for genome-wide projects requiring high specificity and throughput.

Methodology:

Performs a greedy search to generate candidate primers across target loci, evaluates candidates using local and global in silico PCR simulations to identify false priming risks, and applies automated selection rules to output primer sets meeting specificity and efficiency criteria.