ArticleBioinformatics (Oxford, England)2009
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
- Estimating gene conversion rates from population data using multi-individual identity by descent.American journal of human genetics · 2025Article
- A Pedigree-Based Map of Crossovers and Noncrossovers in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- A pedigree-based map of crossovers and non-crossovers in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta).Genome biology and evolution · 2024Article
- The Linkage-Disequilibrium and Recombinational Landscape in Daphnia pulex.Genome biology and evolution · 2022Article
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- High-Resolution Estimates of Crossover and Noncrossover Recombination from a Captive Baboon Colony.Genome biology and evolution · 2022Article
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- A sequentially Markov conditional sampling distribution for structured populations with migration and recombination.Theoretical population biology · 2013Article
- Blockwise HMM computation for large-scale population genomic inference.Bioinformatics (Oxford, England) · 2012Article
- Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias.Molecular ecology · 2012Article
- Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.PLoS genetics · 2012Article
- Fine scale analysis of crossover and non-crossover and detection of recombination sequence motifs in the honeybee (Apis mellifera).PloS one · 2012Article
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- An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.Genetics · 2011Article
- A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.Genetics · 2010Article
- Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome.Molecular biology and evolution · 2010Article
- An approximate likelihood for genetic data under a model with recombination and population splitting.Theoretical population biology · 2009Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationTwo known types of meiotic recombination are crossovers and gene conversions. Although they leave behind different footprints in the genome, it is a challenging task to tease apart their relative contributions to the observed genetic variation. In particular, for a given population SNP dataset, the joint estimation of the crossover rate, the gene conversion rate and the mean conversion tract length is widely viewed as a very difficult problem.
resultsIn this article, we devise a likelihood-based method using an interleaved hidden Markov model (HMM) that can jointly estimate the aforementioned three parameters fundamental to recombination. Our method significantly improves upon a recently proposed method based on a factorial HMM. We show that modeling overlapping gene conversions is crucial for improving the joint estimation of the gene conversion rate and the mean conversion tract length. We test the performance of our method on simulated data. We then apply our method to analyze real biological data from the telomere of the X chromosome of Drosophila melanogaster, and show that the ratio of the gene conversion rate to the crossover rate for the region may not be nearly as high as previously claimed. AVAILABILITY: A software implementation of the algorithms discussed in this article is available at http://www.cs.berkeley.edu/ approximately yss/software.html.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.