Questions tagged [genetic-linkage]
The genetic-linkage tag has no usage guidance.
41 questions
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What software can be used for simulating human meiosis, taking linkage and recombination into account?
I want to study the nature of genetic variation in offspring from the same set of human parents. To this end, I would like to take two (male and female) complete genomes, generate gametes from them, ...
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How can we use the number of crossovers per chromosome to calculate the recombination rate in cM / Mb?
I was reading a paper titled "Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias" (2018). According to this paper:
"The between-species ...
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Why is linkage disequilibrium high on either side of a beneficial mutation, but not between sites across the mutation, during a selective sweep?
I was reading the paper "A survey of methods and tools to detect recent and strong positive selection" (2017) and came across this:
Upon fixation of the beneficial mutation, elevated levels ...
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What does the term "centromere linkage" mean in genetics?
I am currently learning about tetrad/linkage analysis in yeast. I have read two statements similar to this:
If two genes are unlinked, but linked to the centromere the distribution will be 50 ...
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How is a haploblock defined with only one SNP location?
I am reading Impact of estrogen receptor gene polymorphisms and mRNA levels on obesity and lipolysis – a cohort study and am looking at Figure 1. I understand that haplotypes are associated with ...
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What is an intuitive explanation of linkage disequilibrium?
Is it possible to give a simple and intuitive explanation of the concept of linkage disequilibrium? You know, so I can sort of sound like I know what I'm talking about. Everything I read about it has ...
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Gametes produced after single and double cross overs
A female genotype, shown as abc / +++ produces 100 meiotic
tetrads. Among these, 68 showed no cross over (NCO) events; 20 showed
single crossover (SCO1) between a and b; 10 showed single crossover
...
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Are there any phenotypically visible examples of gene linkage in humans?
Are there any examples of two "visible" or "obvious" phenotypic traits in humans that are a priori unrelated, but which tend to be inherited together (i.e. their inheritance ...
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Number of homozygous recessive offspring
A question from the KVPY-SX examination, organised by the Indian Institute of Science (IISc) in Bengaluru, India, held on 3rd November, 2019.
A plant heterozygous for height and flower colour (TtRr) ...
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How can we know which alleles are together on a chromosome?
This illustration says that if the two homozygotes pr+ pr+ vg+ vg+ and pr pr vg vg are crossed to produce a heterozygous offspring (pr+ pr vg+ vg), then:
this cross gives us exactly what we need to ...
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Confusion about how to compute probabilities for linked genes
I am confused about how to compute probabilities for linked genes.
The problem that I am solving is this:
P generation: AAbbddEEff X aaBBDDeeFF. If A and B are 40 centimorgan apart, what is the ...
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Recombination Data Set
I was looking over some genetics question and came across this data set.
In the fruit fly Drosophila melanogaster there is a dominant gene b+ for grey body color and another dominant gene c+ for ...
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Crossover Value and Genetic Mapping [closed]
In my textbook and most of the sources I have checked, it is stated that recombination frequency in eukaryotes give us knowledge on the location of the loci. I don't understand the direct correlation ...
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Help with gene linkage and mapping!
Here's an interesting question I've been trying to figure out:
My annotations are in red. So far, I've figured out:
We know 630 colonies survived when plated with ACD antibiotics...meaning they ...
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How does a neutral allele change relative to a nearby allele under selection?
Suppose I'm looking at a gene being selected against (A) that's decreasing at a rate ($\Delta$P). If there's a nearby allele that is neutral (B) am I correct to assume that B will decrease with A at a ...
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Are SNPs always in linkage disequilibrium with other SNPs
Is it possible to have a SNP that is not found is be non-randomly associating with any other SNP?
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Why do genetic testing companies (FTDNA,AncestryDNA,23andme) express DNA shared in centimorgans (cM) instead of in number of base pairs or in percent?
Expressing DNA shared in number of base pairs or in percent of total genome would be so much simpler and easier to understand for the customers.
.
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Linked genes outcomes in offspring
This question is from a genetics session in my university:
The test cross between a plant with smooth and yellow seeds and a plant with wrinkled and green seeds gives the following results: 140 ...
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Cis and trans linkage
Question:
Two dominant non-allelic genes are 50map units apart, the linkage is:
(A) Cis type
(B) Trans Type
(C) Complete
(D) Absent/Incomplete
My take:
After a lot of searching on the net I found ...
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How to identify whether something is in linkage disequilibrium?
If the following loci indicated the presence of an SNP in flu strains, is Locus 2 and Locus 3, which are located 10 bp apart in linkage disequilibrium?
"When alleles and molecular
markers are ...
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Linkage between chromosomal loci and the Hardy-Weinberg principle
Referring to the Hardy-Weinberg principle, which is always stated with respect to a particular locus on the chromosome, if we observe that two different loci are either always together in Hardy-...
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Non-coding DNA correlation with rate of evolution
Non-coding DNA can be helpful in generating useful mutations that can go on to become new features/functionality of an organism.
Non-coding DNA also indirectly reduces chances of mutation of useful/...
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What exactly is a centimorgan? [duplicate]
Centimorgan's aren't physical distances. The analogy that I could come up with is if you had an array with 10 items,
A = [a, b, c, d, e, f ,g ,h ,i ,j, k]
The ...
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Linkage Disequilibrium - What does it mean when D < 0?
What does it mean when you have a situation where your D<0?
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Sex linked genes?
I am learning about genetics and sex-linked traits. All of the X-linked traits we have considered (eye colour in Drosophila, Duchene Muscular Dystrophy to name a couple)follow the rule that, a female ...
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Calculating gene separation -a genetics problem
I am really struggling with genetics. In particular, I have the following question
Now I am OK with calculating the separation of genes in centrimorgans when I have data like so:
But in the first ...
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What is the exact concept of "Repulsion" and "Coupling" (Genetics)?
From all sorts of books including standard books (like those by Tamarin, Griffith etc) as well as internet; I could not clear-up many things about "Repulsion" and "Coupling". Such as:-
Is "Coupling" ...
user25568
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Is complete linkage found in all four chromosomes or only Y-chromosome of Drosophila? [duplicate]
Male Drosophila shows complete linkage. Is it observed for all four chromosomes or only the Y chromosome?
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Is complete genetic linkage possible?
Linkage is the tendency of genes on the same chromosome to remain together during the process of inheritance. Is it possible that two genes will remain linked generation after generation without any ...
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What test to apply to detect genomic signatures of selection?
I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:
We have three groups: animals exhibiting trait A, trait B and controls....
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Genetic linkage greater than 50 centimorgans
Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant ...
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Cut-off values for LD, LOD and D-prime as algorithmic input
I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP ...
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Mitochondrial D-Loop
I know that the D-loop is a DNA complex in which the strands of double helix DNA molecule are separated for a stretch and held apart by a third strand of DNA. Usually, this third strand has a base ...
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Why does allele linkage cause disproportionate phenotypic ratios? [closed]
I was learning about allele linkage in Biology class and I got confused by the resultant phenotypic ratios.
Say you have a dihybrid cross BbGg x BbGg.
The Punnett square would look like the ...
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How to decide if genes are linked in an unordered mapping problem?
From what I understand, if the tetrads resulting from a cross exhibit the same number of parental ditypes as there are nonparental ditypes, then the genes under consideration are said to be unlinked.
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Linkage disequilibrium D sign
Linkage disequilibrium D equals
$D=x_{11}−p1⋅q1$
where:
Haplotype Frequency
$A_{1}B_{1} = x_{11}$
$A_{1}B_{2} = x_{12}$
$A_{2}B_{1} = x_{21}$
$A_{2}B_{2} ...
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A Genetic linkage problem [closed]
I have recently switched from electronics to computational biology. So having some hard time with my homeworks. Can someone guide me on this problem?
Consider 6 genes A, B, C, D, E, F, G. Some ...
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Possible Genotypes -- Linked Genes
Please consider the following question:
Genes A and B are located on the same chromosome. If two individuals with the genotype shown below are crossed, which genotype could be formed?
Let / ...
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What is the genetic distance where linkage can be ignored?
I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree ...
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recombination frequency problem
Three loci C, D and E are located on the same chromosome in this
order. We found that the frequency of recombinants between C and D is
10% and that between D and E it is 20%. Assuming that ...
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Linkage distance calculation
What is the map unit distance between L and S allele ?
My working : If we take the normal ratio :9:3:3:1 , first one should be 9/16 = 0.5625
and then subtract 0.51 from it, we get 0.0525, similarly ...
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