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Journal Article

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

MPS-Authors
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Odenthal-Hesse,  Linda
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Dutheil,  Julien Y.
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Klötzl,  Fabian
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Haubold,  Bernhard
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

External Resource

http://bioinformatics.oxfordjournals.org/content/early/2016/04/13/bioinformatics.btw195
(Publisher version)

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Fulltext (public)

Odenthal-Hesse_et_al_2016.pdf
(Publisher version), 67KB

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Citation

Odenthal-Hesse, L., Dutheil, J. Y., Klötzl, F., & Haubold, B. (2016). hotspot: software to support sperm-typing for investigating recombination hotspots. Bioinformatics, btw195. doi:10.1093/bioinformatics/btw195.


Cite as: https://hdl.handle.net/11858/00-001M-0000-002B-064D-0
Abstract
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 http://github.com/evolbioinf/hotspot/ CONTACT: haubold@evolbio.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.