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Fraction of Informative Recombinations: A Heuristic Approach to Analyze Recombination Rates
- Source :
- Genetics. 178:2069-2079
- Publication Year :
- 2008
- Publisher :
- Oxford University Press (OUP), 2008.
-
Abstract
- In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 African-Americans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates (ρobs) of 0.85 and 0.37 kb−1 in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of ρobs varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed ∼80% of recombinations in one-third and ∼50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.
- Subjects :
- Recombination, Genetic
Genetics
Likelihood Functions
education.field_of_study
Models, Genetic
Interleukins
Population
Histocompatibility Antigens Class II
Recombination rate
Sequence Analysis, DNA
Investigations
Biology
Sample size determination
Chromosomes, Human
Humans
Computer Simulation
education
Base Pairing
Software
Recombination
Subjects
Details
- ISSN :
- 19432631
- Volume :
- 178
- Database :
- OpenAIRE
- Journal :
- Genetics
- Accession number :
- edsair.doi.dedup.....6776666c163b8caa234c48b9ded2b79c