hotspot: software to support sperm-typing for investigating recombination hotspots

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Motivation: In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a package to support hotspot detection and analysis.

Results: hotspot consists of four programs: asp looks up SNPs and designs allele-specific primers; aso constructs allele-specific oligos for mapping recombinants; xov implements a maximum-likelihood method for estimating the crossover rate; six, finally, simulates typing data.

Availability and Implementation: hotspot is written in C. Sources are freely available under the GNU General Public License from

Supplementary information: Supplementary data are available at Bioinformatics online.

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