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Questions tagged [allele]

Alleles are different forms of many possible alternative forms of the same gene. The different eye colors are for example different alleles of the genes that make the eye color.

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GEN file format, SNPs and alleles

I have a few questions I can't seem to get a straight answer to, regarding the .gen file format and also biology in general. The .gen file format specifies SNPs for individuals. Since each SNP has ...
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Is there a practical upper limit to ploidy?

In my AP Biology class, we were discussing polyploidy, specifically, its deleterious nature in mammals and its prevalence in plants. We also learned that commercial crops, especially fruit, are often ...
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For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?

I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure ...
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Is bi-allelic gene expression random?

Supposing we have the genotypes “Aa”, “AA”, and “aa”... which are not mono-allelic (not imprinted and not X-inactivated). Does the dominance of the “A” allele over “a” allele affect which gene is ...
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Finding specific genotype occurrences given allele frequency

So let's say I have a tetraploid species and I have 4 possible alleles for a particular locus. I have found that I can have 35 total possible genotypes and I know the allele frequencies for each of ...
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What is minor allele frequency, global allele frequency and global minor allele frequency?

Please explain minor allele frequency, global allele frequency and global minor allele frequency in simple words.
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Gene expression: which allele is considered?

For human beings, we have two copies of each gene inherited from the parents. The question is, when referring to gene expression, which copy (or allele) is considered?
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why and how multi allele gets reported during variant calling in vcf?

This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
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Genotypes of gametes produced by an F1 individual?

I have an urgent question as I have an exam tomorrow. I was skimming some past exam papers and one question came up which has me completely confused. A cross was made between a pure breeding ...
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Impact of Natural Selection on Population Size

I have conducted a lab with my IB Biology 11 class, regarding changes in allele frequencies within generations overseeing the natural selection of an advantageous phenotype. We were looking to ...
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Simple Autosomal Recessive question by a novice genetics student

How do you figure the percentage of offspring that will be a carrier of an Autosomal Recessive gene when the FATHER is the recessive carrier and the MOTHER is not affected (normal, no recessive)? ...
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Are mutations the cause of alleles?

For example, some leopards have a mutation which causes black fur. So Black fur and normal fur colour (orange-white) are both alternate forms of the same gene, right? So does that mean that mutations ...
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Hardy-Weinberg sex linked formula

The "big five" assumptions are the ones listed in the main text. However, the basic formulation of Hardy-Weinberg equilibrium also relies on a few other assumptions; Allele and genotype frequencies ...
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How does allele dominance work in polyploid organisms?

You know how there are tables to demonstrate allele dominance in diploids, such as the table found in this question? Well, I was wondering how this works with tetraploids, hexaploids, octoploids, etc....
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How does sexual reproduction generate more genetic variation?

I'm curious as to why sexual reproduction generates genetic variation. For me, the term genetic variation is a little ambiguous. The way I understand it, it's the number of alleles at a locus in a ...
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Hardy-Weinberg for triploids

Problem: A certain species has somatic cells with ploidy 3n (the organism inherits three sets of homologous chromosomes from each of three parents). At a certain locus, there are three possible ...
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Is protein production doubled if you have homozygous dominant genes as opposed to heterozygous genes?

At school we were taught in quite simplistic terms. We were told that there is a dominant and recessive type of every gene and that if the dominant gene was present, the protein is produced and if it ...
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How does selection affect allele frequency?

Question People who are carriers for Blooms Syndrome have developed a selective advantage. How would this affect the allele frequency of the disease allele? My thoughts Natural selection will ...
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how can a recessive allele become represented in a significant number of individuals in a population

Darwin believed that individuals that are poorly adapted to their environment are less likely to survive and reproduce. This means that their genes are less likely to be passed to the next generation. ...
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When to decide that two similar sequences are different genes or not?

Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we ...
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Dominance coefficient

I am trying to understand the meaning of the dominance coefficient. I'll be more specific to what I don't understand, in a moment. Let $A_{11}$, $A_{12}$ and $A_{22}$ be genotypes with fitnesses $1$, $...
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How many allele for one gene are found inside our cell? [closed]

I know it depends on phase. So i am talking of - 1) in human (diploid organism) with cells before prophase (before replication, when 23 pair of homologous chromosomes are present ). I think answer is ...
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Chromosome related problems.

1.) How many versions (alleles) of a gene can we carry if every chromosome is in pair? 2) What happens during the gamete formation (meiosis) ? Do the gene pairs stay together? 3) What happens then ...
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What is a gene transcript, how is it different from an allele?

Within human genetics, My current understanding of a transcript for a particular gene is that it's the exact nucleotide sequence and position of a particular instance of said gene in some individual. ...
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What is allele-specific binding?

So far all I have found is this: https://www.biostars.org/p/132527/ My guess is that some alleles, for whatever reason, bind to things like transcription factors 'moreso' (for want of better word - ...
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What are multiallelic genes?

Is there a clear detailed description for multiallelic genes? Are they simply genes that are more than two alleles?
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Minor Allele Frequency (MAF) higher than 0.5?

I have a set of data in PLINK format (*.bed, *.bim and *.fam files). There are around 2000 individuals in my dataset. I used PLINK to calculate allele frequencies in the population: p-link --bfile ...
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Is this how female and male gametes look like in plants?

In the red box, the pink one is female sex cell I presume and the blue one is a male sex cell. http://prntscr.com/dsii2x Am I right? or are these chromosomes.. I'm confused. This is law of ...
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Is the term 'allele' specific to sexual populations?

I had always thought that 'allele' simply meant a variant of a gene and thus could be used in the context of either asexual or sexual populations. With it only being slightly less useful as a concept ...
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Interpreting Allele frequency and allele count

In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never ...
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Passing on Alleles

Just a basic question on alleles, I am just trying to learn the basic concepts. So if we are to screen two parents, both with one dominant and one recessive allele for a given characteristic e.g. eye ...
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“Genotype structure”?

What does a geneticist mean when they write "genotype structure", e.g. the sentence "...represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected ...
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How to recognise the type of allele by pedigree analysis diagrams? [closed]

It was said that this interference pattern is due to dominant allele. I fail to see that. In general how to recognise the type of allele by pedigree analysis diagrams?
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How allele is related to trait that is more complex than two cases (ex. height)?

Recently I started to learn about evolution and genetics. Simple stuff at the beginning - some videos, some reading. So far, everything seems to be pretty simple and straightforward. I easily grasp ...
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Recessive is Dominant to Dominant?

If a gene has for instance three alleles, p, q, and r, then could p be dominant to q, q be dominant to r, but r be dominant to p? Can a gene that is recessive to one allele not be dominant to another ...
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Relationship between genetic diversity within and between species

Here is a quote from Wagner (2008) A second line of evidence [against neutralism] comes from the relationship between the mean number of polymorphic differences between alleles within a species, $\...
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Genetic mutations and new alleles

Amongst silent, nonsense and missense genetic mutations, is the latter the only one that leads to the creation of new alleles? If we define alleles as a specific form of a gene, and a gene as a ...
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Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome?

There are many sources that say that genes that are "linked" by being on the same chromosome assort with each other -- that when an allele is passed on that the gamete containing said allele will also ...
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Are alleles equally sized?

If alleles occur at the same locus on a chromosome, does that mean they are of the same size? I was under the impression that they were, but I saw a gel electrophoresis testing different alleles of ...
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What is the best test for SNV clustering?

I am looking for a method to cluster single nucleotide polymorphisms based on clinicopathologic data (mainly receptor immunoistochemistry). So far, I've came up with only two that handle dummy ...
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Calculating pairwise Fst from allele frequencies

I am trying to refresh my memory on population genetics for a project, and I'm having some trouble. Assume I have genetic data on 3 populations with 5 individuals in each of a given species, with the ...
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Chance of child inheriting at least one copy of an allele - heterozygote mother, unknown father

Our genetics professor has posted up working for previous examination answers, but I am not convinced that his answer is correct. My answer is close but may just be due to co-incidence. Question: ...
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Why do almost all SNPs have two alleles?

Reading the Wikipedia page for SNPs I find the sentence "Almost all common SNPs have only two alleles." This is consistent with terminology elsewhere, such as the therm "Minor allele frequency", which ...
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Albinism inheritance problem: what are the father's alleles if he got an albino kid?

Albinism is caused by a recessive gen "c". A normal man marries an albino woman. The first son happened to be albino. What are the possible phenotypes of the parents? What is the chance that their ...
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Recessiveness of allele for protection of organism

Heterozygous organisms profit from pairs of gene alleles. Harmful alleles when being recessive can be carried without any harm for the organism. Only when two harmful recessive alleles form a gene the ...
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Recessive alleles at Hardy-Weinberg equilibrium

I've run into a question that I disagree with others on but I would like to receive the input of others. The question is: If a population is at Hardy-Weinberg equilibrium, which of the following can ...
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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 does the molecular machinery choose where to cut a chromosome for recombination?

I'm wondering about a few technicalities of crossover in meiosis. The point of crossover is to create new chromosomes that don't have the same allele combinations as the original two chromosomes. ...
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Mode of Enzymatic Inhibition via R-Allele

The photo above shows the effects of the R allele of the pea shape gene on the synthesis of an enzyme that converts unbranched starch into branched starch. The r allele of this gene determines an ...
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Microsatellite shifts (peak calling) GeneMapper! Thesis help!

I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide ...