A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data
2009
Bioinformatics
Preserved Fulltext
Title Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. ...
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 ...
ACKNOWLEDGEMENTS We thank Jo Gay for making her source code available to us and Charles H. Langley for providing us with the su(s) and su(w a ) data. ...
doi:10.1093/bioinformatics/btp229
pmid:19477993
pmcid:PMC2687983
fatcat:nugabrozyjdkvfpy4kpf47z7pm
Estimating the Rate of Gene Conversion on Human Chromosome 21
2004
American Journal of Human Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
The estimated ratio of gene-conversion rate to crossing-over rate has a range of 1.6-9.4, depending on the assumed conversion tract length (in the range of 500-50 bp). ...
In addition to being computationally feasible for very large data sets, these summaries were designed to yield robust estimates of gene-conversion rates in the presence of variation in crossing-over rates ...
We also thank Jeff Wall, Noah Rosenberg, and Chris Toomajian for helpful suggestions and comments about the manuscript. ...
doi:10.1086/423451
pmid:15250027
pmcid:PMC1182018
fatcat:k4sihoivujairpr4zbkliuzzje
Meiotic gene-conversion rate and tract length variation in the human genome
2013
European Journal of Human Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
parameters (ie, rates and mean tract lengths) remains far from complete. ...
Here, we apply this new method to SNP data from multiple human populations and attempt to characterize for the first time the fine-scale variation in gene-conversion parameters along the human genome. ...
They estimated that gene-conversion occurs at a rate of 4-15 times the crossing-over rate and mean tract lengths are in the range of 54-132 bp. ...
doi:10.1038/ejhg.2013.30
pmid:23443031
fatcat:x565sakm4fggjeztn6c4zp6svy
Bayesian Population Genomic Inference of Crossing Over and Gene Conversion
2011
Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The mean tract lengths for gene-conversion events are estimated to be 70 bp and 430 bp, respectively, for these data sets. ...
Here, we describe a coalescent-based full-likelihood Markov chain Monte Carlo (MCMC) method for jointly estimating the crossing-over, gene-conversion, and mean tract length parameters from population genomic ...
crossing-over rate, the population gene-conversion rate, and the mean conversion tract length from SNP data. ...
doi:10.1534/genetics.111.130195
pmid:21840857
pmcid:PMC3189816
fatcat:qcpkme2rlncdvfdkx2t3e4xzx4
Hypothesis testing of meiotic recombination rates from population genetic data
2014
BMC Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Meiotic recombination, one of the central biological processes studied in population genetics, comes in two known forms: crossovers and gene conversions. ...
Conclusions: Our methodology provides a necessary complement to the existing procedures of estimating meiotic recombination rates from population genetic data. ...
An allocation of computer time from the UA Research Computing High Performance Computing (HPC) and High Throughput Computing (HTC) at the University of Arizona is gratefully acknowledged. ...
doi:10.1186/s12863-014-0122-7
pmid:25433522
pmcid:PMC4267743
fatcat:czsinh535ze2xf2ecin73umwg4
Segmental duplications and gene conversion: Human luteinizing hormone/chorionic gonadotropin gene cluster
2005
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
The data highlight an important role of gene conversion in spreading polymorphisms among duplicon copies and generating LD around them. ...
Apart from a few well-characterized regions (MHC, -globin), the diversity and linkage disequilibrium (LD) patterns of duplicons and the role of gene conversion in shaping them have been poorly studied ...
In contrast, the estimated ratio of geneconversion to crossing-over rate depended inversely on the conversion tract length: As the length of the tract decreases, the estimated rate of gene conversion increases ...
doi:10.1101/gr.4270505
pmid:16251463
pmcid:PMC1310641
fatcat:cs3jzx3ezvbwzkupc5hcfbjdfe
Coalescent framework for prokaryotes undergoing interspecific homologous recombination
2018
Heredity
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Using this simulation tool, msPro, we observed that the joint processes of intra- and interspecific recombination generate complex SNP patterns. ...
The insight gained from our work using the msPro simulator will be useful for understanding and evaluating the relative contributions of intra- and interspecific recombination events in generating complex ...
Acknowledgements The authors very much thank the three reviewers for their useful and kind comments that improved the manuscript. ...
doi:10.1038/s41437-017-0034-1
pmid:29358726
pmcid:PMC5889408
fatcat:lafu46em3nfwpnx4vnbzqgjjza
A Novel Method with Improved Power To Detect Recombination Hotspots from Polymorphism Data Reveals Multiple Hotspots in Human Genes
2005
American Journal of Human Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We apply the method to data from 89 genes sequenced in African American and European American populations. ...
We introduce a new method for detection of recombination hotspots from population genetic data. ...
We particularly thank one of the reviewers for the idea of how to estimate g.
Web Resources The URLs for data presented herein are as follows: Cosi, http://www.broad.mit.edu/personal/sfs/cosi/ P.F.' ...
doi:10.1086/497579
pmid:16252238
pmcid:PMC1271387
fatcat:judybthgf5ddjbjiz6ecbblkie
Biased Gene Conversion Skews Allele Frequencies in Human Populations, Increasing the Disease Burden of Recessive Alleles
2014
American Journal of Human Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb z 0.05 to 0.09. ...
Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data ...
Introduction Meiotic recombination results in either crossover or noncrossover events, and gene conversion can occur in either case. 1 In humans the mean tract length of these gene conversion events ...
doi:10.1016/j.ajhg.2014.09.008
pmid:25279983
pmcid:PMC4185123
fatcat:7s7yqdugy5afdpht7j54kbi5x4
Estimating the rates of crossover and gene conversion from individual genomes
[article]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Our analyses show i) that the rates of crossover and gene conversion can be accurately co-estimated at the level of individual chromosomes and ii) that previous estimates of the population scaled rate ...
We present heRho, a simple composite likelihood scheme for co-estimating the rate of crossover and gene conversion from individual diploid genomes. ...
SE is supported by an EastBio studentship from the British Biological Sciences 19 ...
doi:10.1101/2021.11.09.467857
fatcat:t5lrwtbd5fbchaie36c3eh4s3m
A Whole-Chromosome Analysis of Meiotic Recombination in Drosophila melanogaster
2012
G3: Genes, Genomes, Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Mean gene conversion tract lengths were estimated to be 476 base pairs, yielding a per nucleotide conversion rate of 0.86 × 10(-5) per meiosis. ...
Both of these values are consistent with estimates of conversion frequency and tract length obtained from studies of rosy, the only gene for which gene conversion has been studied extensively in Drosophila ...
W.D.G. was supported by URC and FSRG grants from the DePaul University College of Liberal Arts and Sciences. J.P.B. was supported by the University of Kansas and NSF Award MCB-1022165. ...
doi:10.1534/g3.111.001396
pmid:22384403
pmcid:PMC3284332
fatcat:hersyw6l65gzlmjyjgbp2olnuu
Fast and flexible simulation of DNA sequence data
2008
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
Acknowledgments This research was funded by National Institutes of Health grants HG004049 (P.M and J.D.W) and R25T CA112355 (G.K.C. Fellow). ...
If the next event is a gene conversion event, we generate the tract length and add to the graph the first crossover event of the gene conversion. ...
Briefly, we used data from the NIEHS SNPs project (Livingston et al. 2004 ) to estimate demographic parameters under a two-population model meant to mimic the history of West African and European populations ...
doi:10.1101/gr.083634.108
pmid:19029539
pmcid:PMC2612967
fatcat:j72f7hqyk5ay5erdiyz6vp3fcm
The Recombinational Landscape in Daphnia pulex
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
on haplotypes and long-range gene-conversion-like processes. ...
AbstractThrough the analysis of linkage disequilibrium from genome-wide sequencing data for multiple individuals from eight populations, the general features of the recombinational landscape are revealed ...
Assuming an exponential distribution of conversion tract-lengths with mean L, the recombination rate between sites is conversion-tract lengths (on the order of 10 kb) cause the first inverse-scaling relationship ...
doi:10.1101/2020.03.03.974485
fatcat:egxcvpsl5bhh7laeylazi4zkyu
Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes
2017
Nature Communications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
, with a corresponding non-crossover gene conversion rate of 8.75 ± 0.05 × 10 −6 per base pair per generation. ...
Using exome sequences from 3222 British-Pakistani individuals with high parental relatedness, we estimate a mutation rate of 1.45 ± 0.05 × 10 −8 per base pair per generation in autosomal coding sequence ...
Born in Bradford is only possible because of the enthusiasm and commitment of the Children and Parents in BiB. ...
doi:10.1038/s41467-017-00323-y
pmid:28827725
pmcid:PMC5566399
fatcat:gk7xgp7pprbzteb6rlz6dofiyi
Contrasting Methods of Quantifying Fine Structure of Human Recombination
2010
Annual review of genomics and human genetics (Print)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
These maps, which are derived from estimates of linkage disequilibrium (LD), rely on population genetics theory to relate the decay of LD to the local rate of recombination, but other population processes ...
The LD maps have a level of resolution greatly exceeding that of the pedigree maps, and at this fine scale, sperm typing allows a means of validation. ...
Steve Buyske (Rutgers University) for helpful discussions and analyses. This work was supported by National Institutes of Health (NIH) grants GM065509, HG003229, and MH084685. ...
doi:10.1146/annurev-genom-082908-150031
pmid:20690817
pmcid:PMC2980829
fatcat:movsos2ttrcmllzev4e76timuu
« Previous
Showing results 1 — 15 out of 2,069 results