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

Odenthal-Hesse, L., Dutheil, J. Y., Klötzl, F., & Haubold, B. (2016). hotspot: software to support sperm-typing for investigating recombination hotspots. Bioinformatics, 32(16), 2554-2555. doi:10.1093/bioinformatics/btw195.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002B-064D-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-1A8E-F
Genre: Journal Article

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Odenthal-Hesse_et_al_2016.pdf (Publisher version), 67KB
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Odenthal-Hesse, Linda1, Author              
Dutheil, Julien Y.2, Author              
Klötzl, Fabian3, Author              
Haubold, Bernhard3, Author              
Affiliations:
1Research Group Meiotic Recombination and Genome Instability, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2355693              
2Research Group Molecular Systems Evolution, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2068287              
3Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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 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.

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Language(s): eng - English
 Dates: 2016-03-242016-02-082016-04-072016-08-152016-08
 Publication Status: Published in print
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 Identifiers: DOI: 10.1093/bioinformatics/btw195
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 32 (16) Sequence Number: - Start / End Page: 2554 - 2555 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991