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

Abstract

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. 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. hotspot is written in C. Sources are freely available under the GNU General Public License from http://github.com/evolbioinf/hotspot/ haubold@evolbio.mpg.de Supplementary data are available at Bioinformatics online.