All Questions
74 questions
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How to test whether correlation of couples phenotypes is due to assortative mating or environment?
A few phenotypes are easier to pinpoint as assortative mating (height for example), But other phenotypes such as vitamin D, weight, etc could be a combination of shared environment and assortative ...
- 121
3
votes
0
answers
17
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How to model the relationship between environments based on environmental covariates in a genomic prediction context
I have a dataset with different wheat lines in multiple environments. For each line various traits are measured (e.g. grain yield). I am trying to set up various genomic prediction models (linear ...
- 31
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1
answer
48
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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, ...
- 157
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1
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52
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Calculation for underlying genetic value of a phenotype given parents genetic values
What is the most accurate way to calculate a child's genetic predisposition to a phenotype, given both parents' genotypic predispositions?
Assume trait X is 50% heritable and controlled by an ...
- 401
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0
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19
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Are there limitations in using DNase I hypersensitive sites (DHSs) to identify candidate enhancers?
Candidate enhancer regions are often defined in studies by DHSs and/or certain chromatin marks. I was wondering if DHSs are exhaustive for identifying possible enhancer regions, and if there is any ...
- 11
3
votes
1
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125
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How can SNP arrays be used to detect deletions within a gene?
I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
- 1,761
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2
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81
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How many people need to have the same mutation of a gene in order for that gene to be seen as a feasible candidate for a disease?
I am learning about genome-wide association studies (GWAS) and I know that they are used to see whether certain SNPs are associated with a disease of interest. From everything that I have watched and ...
- 1,761
1
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1
answer
55
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Can CNVs have a phenotypic effect unrelated to the direct modification of transcriptional units?
I'd like to know how (or if) copy number variations can have a phenotypic effect unrelated to the direct disruption/movement/duplication of sequences for coding regions, promoters, enhancers etc.
I ...
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-4
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1
answer
96
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metaphors for explaining the role of DNA in the cell [closed]
Various metaphors are used to explain the central role of DNA in a cell to laypersons. These include blueprint, recipe, catalogue, instruction manual etc. I even heard someone describing DNA as a '...
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1
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409
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How to identify an unknown species from its genome sequence [closed]
I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to ...
- 186
3
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1
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324
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Is this basic gene diagram correctly labeled?
I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...
- 131
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2
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56
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What's the difference between the terms "gene map" and "genome"?
It seems some sites arbitrarily restrict "gene map" to only a single chromosome, but others don't. Supposing we don't restrict it to just a single chromosome, is it different from "genome"? Are these ...
- 123
1
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1
answer
2k
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What is a Singleton Variant
I'm reading a paper that on a population genetics study where they sequence a number of genomes. The study states that 101 Singleton Variants per individual where found. What does Singleton mean?
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votes
1
answer
47
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Consider gene is countable, can anyone give a concrete example of "a gene"?
gene is a countable noun but people always say genes, so what is A gene?
for instance, Each chromosome contains many genes, so, which part of the chromosome of Escherichia coli could be ...
- 99
1
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1
answer
59
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How are haplotype blocks different from genes?
According to Cardon et al. 2003, a haplotype block is
A discrete chromosome region of high linkage disequilibrium and low
haplotype diversity. It is expected that all pairs of polymorphisms
...
- 819
1
vote
1
answer
87
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What is the cause of "imbalanced" linkage disequilibrium?
With perfect linkage disequilibrium ($D' = 1, R^2 = 1$), you might have the following table of counts for the alleles:
B b
A 100 0
a 0 100
With "...
- 133
0
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1
answer
53
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Understanding genetic similarity in humans [duplicate]
I was reading "Blueprint" by Robert Plomin (online preview on webpage) and got stuck when I got to these two sentences in the prologue:
"We are the same as every other human being for more than 99 ...
- 1
1
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2
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201
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In marine DNA viral diversity studies, what would "paradigm of rampant mosaicism" refer to?
The recent paper in Cell Marine DNA Viral Macro- and Microdiversity from Pole to Pole describes the (huge) new Global Ocean Viromes 2.0 (GOV 2.0) dataset.
In the Results and Discussion section, the ...
- 5,572
1
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0
answers
27
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How do researchers define the region a lead SNP encompasses?
As I understand it, a lead SNP captures the variance for all unmeasured SNPs in a region due to it's low p-value and high linkage disequilibrium. However, in different papers the region size differs (...
- 133
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1
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63
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What are primary reasons for the failure to localise/anchor sequences in genome assemblies?
My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo ...
- 53
1
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1
answer
177
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What exactly does the phrase "chimerical sharing" mean in this abstract?
The Gizmodo article Australian Siblings Are Semi-Identical Twins, Some of the Rarest Humans Ever links to the new paper in NEJM Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning ...
- 5,572
-2
votes
1
answer
187
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Intelligence as measured by DNA tests
Suppose a person has an IQ of 130, as measured by a standard IQ test, when he is 18 years old. He then goes on to develop severe mental illness, which reduces his IQ to 100. After this, he takes a DNA-...
- 363
1
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0
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38
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What percentage of genome do slugs and scallops have in common?
We can know genetic distance of thousands of species. The OTT tree of life gives genetic distance for nearly all species. Is there a resource to compare the genomes of any sequenced animals to know ...
- 10.5k
3
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90
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Why are animal mitochondrial genomes so conserved and small in comparison to those of plants?
Background
Levings and Brown (1989):
Higher plant mitochondrial genomes are much larger and
more complex than those of other organisms. They vary
in size from about 200 kb in Brassica species ...
- 68.3k
0
votes
2
answers
156
views
What is the likelihood of a single human gene to the same gene from the other human?
The human genome comprises 3,234.83 Megabases and contains ~ 19,000 genes. It has been estimated that the genomes of humans are 99.9% identical. How likely is it that any single gene might vary from ...
- 11
1
vote
1
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605
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What is meant by genomic imprinting being reversible?
I'm not trying to understand the underlying molecular processes, rather understand it conceptually.
This is what it says in my coursebook:
"The imprint, obtained during gametogenesis, is ...
- 113
2
votes
2
answers
313
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Actual determination of the DNA sequence in the shotgun approach?
I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
- 143
6
votes
2
answers
613
views
Which DNA elements belong to the definition of a gene?
I see a lot of different DNA elements mentioned as part of a gene (talking about eukaryotes):
The length of DNA following the promoter is a gene and it contains the
recipe for a protein. (video)
...
- 2,410
2
votes
1
answer
110
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Excluding the Exon, What Does the Rest of the Genome Do?
The exon is the portion of the genome that encodes protein synthesis, if I understand correctly.
But, this exon is apparently less than 5% of the genome.
So, what does the rest of the genome do?
- 337
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1
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631
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Two sets of chromosome and the sequencing output
Humans have two sets of chromosomes that are not connected in each cell. Am I correct?
I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some ...
- 41
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0
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33
views
DNA Sequencing and genotyping [closed]
Before going to the details of the question let me post a few other details-
(I posted something similar and got no useful answers-probably because I didn't explain things properly or something else)-
...
- 41
1
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0
answers
34
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Quantifying the number of fragments from RAD library
I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
- 121
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3
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13k
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How is the size of a gene defined?
Is there an agreed definition as to how many nucleic acid bases constitute a gene?
If not, why not? I'm not sure I understand how the exact sizes of genes are defined.
- 529
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311
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Perplexing by the way of estimating the shared or different genes between humans and chimps
We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred ...
- 99
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1
answer
177
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Current state of Gene Therapy [closed]
I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood.
(i) Are there approaches ...
user24161
-2
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2
answers
1k
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When is gene density an important parameter in experiments?
As per wikipedia definition, gene density is defined as:
"In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in ...
- 391
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2
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183
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How do biologists quantify "gene expression" in experiments?
I've read papers which contain statements such as "control of gene expression is critical in biological processes".
How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
- 529
1
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0
answers
47
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What further research can the result of gene variation detection be used for [closed]
We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
- 11
2
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0
answers
366
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RAD sequencing: choosing the appropriate enzyme?
I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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5
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1
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533
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What is meant by "the degree to which a gene is expressed" in an individual?
Here is an excerpt from a text that I was reading,
Here is an example of microarray data. The idea is to take a group of
different individuals and for each of them, you measure how much they
do ...
- 153
4
votes
2
answers
1k
views
Do transposons usually jump from one chromosome to another?
If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?
- 43
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1
answer
55
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A trivial question on the meaning of "relatives" in an article on horizontal gene transfer
Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind?
DETECTION OF HORIZONTAL GENE TRANSFER
There are ...
- 1,309
2
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1
answer
145
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Are dogs affected by dwarfism?
My husband and I noticed a dog today that looked like a smaller version of a purebred Border Collie, although it didn't appear to be a puppy. It made us wonder if other animal species experience ...
- 3,084
1
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1
answer
831
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(Genetics) Is a silencer the same as gene silencing (heterochromatin)?
Is silencer the same as gene silencing?
I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
- 31
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1
answer
107
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Solid mouse (C57BL/6) WT primers
I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing?
Alternatively, I thought of just ...
- 1,352
2
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1
answer
80
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Understanding conclusions that functional regions are under negative selection?
I am reading in notes for a comparative annotation lecture that :
all DNA is subject to mutations
most functional regions are under negative selection (ie., mutations are often deleterious)
The ...
- 1,289
0
votes
1
answer
70
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Supercomputer and undergraduates [closed]
Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. ...
- 9
1
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1
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88
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RNAs arising from intergenic regions
Which type of RNA molecule is coded for in intergenic regions? I think it must be a non-coding RNA but I'm unsure which type.
- 167
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1
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78
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Where can I upload non-human Genotype data?
I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype ...
- 121
4
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1
answer
63
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Is there an association between environmental and mutational robustness?
The robustness of a genotype is the ability of this genotype to resist (always produce the same phenotype) to various parameters such as mutations and environment. The ability of a genotype to resist ...
- 68.3k