All Questions
73
questions
3
votes
0
answers
16
views
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
0
votes
1
answer
45
views
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
0
votes
1
answer
38
views
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
1
vote
0
answers
17
views
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
answer
105
views
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 ...
- 1,741
0
votes
2
answers
76
views
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 ...
- 1,741
1
vote
1
answer
55
views
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 ...
- 11
-4
votes
1
answer
76
views
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 '...
- 33
0
votes
1
answer
332
views
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
votes
1
answer
294
views
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
0
votes
2
answers
53
views
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
vote
1
answer
2k
views
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?
- 13
-1
votes
1
answer
45
views
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
vote
1
answer
54
views
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
86
views
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