hotspot

hotspot detects recombination hotspots and analyzes sperm-typing data to identify recombinant chromosomes and estimate crossover rates.

Key Features:

• Automated primer design (asp): Looks up single nucleotide polymorphisms (SNPs) and designs allele-specific primers for allele-specific PCR assays.
• Allele-specific oligo construction (aso): Constructs allele-specific oligos for mapping recombinant chromosomes and identifying crossover breakpoints.
• Crossover rate estimation (xov): Estimates crossover rates at recombination hotspots using a maximum-likelihood statistical method.
• Simulation of typing data (six): Simulates sperm-typing datasets to model expected outcomes for experimental design and interpretation.

Scientific Applications:

• De novo recombinant detection: Enables detection of de novo recombinants at recombination hotspots using allele-specific PCR assays.
• Quantification of recombination: Provides estimates of crossover frequency and distribution at hotspots for population- and species-level analyses.
• Experimental planning and validation: Uses simulated sperm-typing data to plan assays and assess statistical power for hotspot mapping studies.

Methodology:

Implemented in C and employs a maximum-likelihood method for crossover-rate estimation.