Questions tagged [genomics]

The study of genomes, the DNA complement of organisms.

Filter by
Sorted by
Tagged with
2 votes
1 answer
38 views

No. of genes and organismal complexity?

Why do humans contain trillions of cells arranged in many complex organs, and worms contain many less cells and less organs, but we and the worm have a similar number of genes? See for example Table 1 ...
li tchi.'s user avatar
0 votes
1 answer
44 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, ...
actinidia's user avatar
  • 157
0 votes
1 answer
45 views

Can a gene transfer from a plasmid to a bacterial chromosome?

Plasmids are involved in providing resistance to antibiotics. So, can that gene or any other gene transfer from the plasmid to the bacterial chromosome? Is there any chance where antibiotic resistance ...
Amit Kumar's user avatar
0 votes
0 answers
26 views

How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation?

From 'Protein and DNA Sequence Determinants of Thermophilic Adaptation', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | https://doi.org/10.1371/...
Growing6884's user avatar
1 vote
2 answers
123 views

How many generations does it take for the average descendant not to be genetically related to the ancestor?

Parent 1 and 2 have children. Assume infinite, randomly-mating population size. How many generations until the median descendant by lineage of parent 1 has 0 base pairs inherited from parent 1? I ...
BigMistake's user avatar
0 votes
1 answer
37 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 ...
BigMistake's user avatar
2 votes
1 answer
54 views

Why is SF3B3 gene annotation missing in chm13_v2 gff3 file, and is it temporary?

In the annotation gff3 provided for CHM13 v2, I noticed that for the SF3B3 gene there's no entry with type "gene" (third column). However, transcripts and other annotations are still ...
gc5's user avatar
  • 820
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 ...
rintsen's user avatar
  • 11
0 votes
1 answer
64 views

What does ‘per DNA fragment’ mean?

In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the DNA sequencing: In living cells, DNA rarely exists in isolation; it is typically bound tightly to ...
Ahmed Samir's user avatar
3 votes
1 answer
100 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 ...
ceno980's user avatar
  • 1,701
0 votes
0 answers
77 views

Why people carrying the same SNP doesn't have the same Promethease report

I'm a frequent user of Promethease to run health analysis based on MyHeritage SNP data dump. I ran two people through Promethease and both have the same SNP: ...
ppaulojr's user avatar
  • 101
2 votes
0 answers
59 views

Why are bacterial genomes limited in size compared to eukaryotic ones?

I was looking at this graph that shows that the eukaryotic genome has "no size limit" whilst the bacterial one does. Unfortunately the graph has no reference but essentially the idea is that ...
terraregina's user avatar
0 votes
2 answers
73 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 ...
ceno980's user avatar
  • 1,701
1 vote
1 answer
87 views

Translating either rs number or genomic position to either a residue in the DNA or in the amino acid sequence

Studying Schizophrenia and reading some papers discussing polymorphisms in the 5HT-2A receptor gene (HTR2A). Specifically, the authors mention A-1438G, T102C, his452tyr. How does one best take ...
neurosciencecalc's user avatar
2 votes
1 answer
92 views

Transcript without a start codon in mouse genome?

I am looking at the mouse reference genome in combination with ensemble annotation and am finding many transcripts that have no start codon. For example, the transcript ENSMUST00000193149 at position ...
subhacom's user avatar
  • 123
2 votes
1 answer
57 views

How to calculatie frequency of recombination between two genes based on their coordinates in ENSEMBL?

I have two genes: https://www.ncbi.nlm.nih.gov/gene/326619 and https://www.ncbi.nlm.nih.gov/gene/326620 both are mapped to chromosome 13. First is at position 23944778..23945232 second is at positions ...
Pavel Shliaha's user avatar
1 vote
2 answers
572 views

Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Any comparable alternatives to linked read sequencing? I read that 10X Genomics discontinued its linked-reads technologies: Discontinuation of Linked-Reads At 10x Genomics, we are committed to ...
ilam engl's user avatar
  • 294
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 ...
snord's user avatar
  • 11
5 votes
3 answers
1k views

Can one identify an organism based on its genome alone?

If one is given the complete genome of some unknown organism, would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a ...
Ayman Alhourani's user avatar
9 votes
2 answers
488 views

Tips for longer fragment size and higher purity of insect DNA

Aim In a pilot experiment I tested three different genomic DNA extraction methods on the non-model organism Pieris mannii (southern small white; Insecta, Lepidoptera, Pieridae). The goal was to ...
CorinaPlus's user avatar
-1 votes
2 answers
64 views

Can the metatranscriptomics replace the approach of functional metatranscriptomics/functional metagenomics?

While metatranscriptomics reveals information about the expression of genes and their functions too, Functional metatranscriptomics (https://www.nature.com/articles/ismej201167) allows the ...
Noor Elhouda's user avatar
5 votes
2 answers
148 views

Are there known genome sequencing issues in E. coli?

Despite the fact that the human genome project was declared "complete" in 2001, there are even now still gaps due to difficult-to-sequence regions of the genome such as telomeres and ...
jakebeal's user avatar
  • 6,977
1 vote
0 answers
29 views

Chromosome Deletion Notation in Cancers

The cancer literature often refers to the deletion of certain sections of a chromosome (e.g. "17p del" or "Del(17p)" for the deletion of chromosome 17's p-arm.) Does this mean both ...
Erich Peterson's user avatar
-4 votes
1 answer
55 views

Finding All of the Genes in a given Genome

I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout ...
Chris's user avatar
  • 35
-4 votes
1 answer
69 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 '...
haz's user avatar
  • 109
2 votes
1 answer
48 views

Questions about Cohesin - what does the ATPase domain do, and any suggested PDBs to look at?

I've been reading about cohesin lately, and I'm confused about the head subunit interactions. I've read a few papers, and also found this nice figure from wiki that demonstrates the crux of my ...
Chris's user avatar
  • 35
0 votes
1 answer
296 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 ...
Biochem's user avatar
  • 186
0 votes
1 answer
71 views

Why are there different gene expressions that are refered to the same gene in microarray experiments results?

I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
Manuela's user avatar
  • 443
0 votes
2 answers
180 views

What exactly is "chromosome topology"?

I've been reading a lot about Hi-C lately, and this has been bothering me. So far as I can tell from reading around, the topology is related to the conformation of the linear chromosome. This seems ...
Chris's user avatar
  • 35
-1 votes
1 answer
36 views

Truncated ORF3a protein of SARS-CoV2! Why? How does it formed?

Across the world so far, we have three truncated ORF3a proteins in SARS-CoV2 in India only. Can you illuminate me how does a protein (here accessory protein of SARS-COV2) generally get such nonsense ...
Sk Sarif Hassan's user avatar
0 votes
1 answer
53 views

What is the copy number of a given gene in GRCh37?

sorry for the naive question, but how do I determine what the copy number is in GRCh37 for a gene with multiple CNVs? (e.g. DRD4).
krstn's user avatar
  • 113
2 votes
0 answers
59 views

Interpretation of Pangenome: high number of accessory genes

I performed a pangenomic analysis on a collection of 52 strains belonging to the same genus (some 5-6 different species). All the strains were isolated from the same environment: interior compartment ...
Rob's user avatar
  • 21
3 votes
1 answer
279 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 ...
Alex Walczak's user avatar
1 vote
2 answers
128 views

Genomic location-coordinate of RdRp of SARS-CoV2

I understand that nsp12 is the RdRp protein in the ORF1 of SARS-CoV2 genome. And nsp12 starts from the starting nucleotide base of orf1ab. Could you please tell me the exact genomic location ...
Sk Sarif Hassan's user avatar
0 votes
1 answer
236 views

Self-study genetics

I'm new at the field of genomics. I'm a theoretical physicist by training and now we would like to translate some of the ideas to the DNA, possibly in real genomic instances. The concrete example ...
user2820579's user avatar
5 votes
1 answer
491 views

Where can I find SARS-CoV-2 genome sequences for the UK?

I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not ...
Steve Crawford's user avatar
3 votes
3 answers
2k views

Is it possible to distinguish between coding and template strands from the sequence?

Let’s say you have the following DNA sequence fragment: 5’-ACCAGTACTTCGT-3’ 3’-TGGTCATGAAGCA-5’ Is there any way to determine which strand is the template ...
Diafotismos's user avatar
0 votes
1 answer
48 views

Embryonic cells, when can you detect them in vivo? (In order to do whole genome sequencing)

I was wondering, when is it possible to extract cells (humans or mice) in order to sequence them and detect diseases. Extra: Urine of the embryo in humans is excreted in the 16th week, so I guess that ...
Héctor's user avatar
  • 19
2 votes
3 answers
97 views

Which side of the DNA helix is used for describing SNPs?

In genetic research I often come across references to single-nucleotide polymorphisms (SNPs). An example is rs3184504(C;T). As far as I understand it: In this ...
feetwet's user avatar
  • 795
-1 votes
1 answer
73 views

How do different genes on human genome express themselves?

It is said that human genome contains over twenty five thousand genes, How many of these (can) express themselves as an external or internal trait in human beings (for e.g. like eye-colors, hair ...
Aryan Gupta's user avatar
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 ...
Aero's user avatar
  • 123
1 vote
1 answer
1k 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?
A. Aguirre's user avatar
1 vote
0 answers
39 views

Single-cell ATAC seq arrays

As part of a data analysis project, I encountered two kinds of single-cell assays for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial ...
youngtableaux's user avatar
4 votes
0 answers
84 views

Is mating between human and non-human primates theoretically possible? [duplicate]

I wonder if it is theoretically achievable to produce living offspring between a human and a non-human primate. Great apes have 24 pairs of chromosomes compared to our 23, however, it is known that a ...
blu potatos's user avatar
-1 votes
1 answer
38 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 ...
czlsws's user avatar
  • 99
0 votes
1 answer
15 views

Where to download confier (pine) or A. thaliana annotated reference RNA transcriptomes in full .gbk (GeneBank) format?

Where to download confier (pine) or A. thaliana annotated reference RNA transcriptomes in full .gbk (GeneBank) format?
player777's user avatar
  • 111
1 vote
1 answer
52 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 ...
M. Beausoleil's user avatar
-1 votes
1 answer
94 views

difference between population genetics and genomics

I don't have a biological question therefore, this might be be quite basic. But I want to know does genomics entail population genetics or these are completely different fields?
Shafa Haider's user avatar
1 vote
1 answer
85 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 "...
Betterthan Kwora's user avatar
0 votes
1 answer
53 views

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 ...
j o's user avatar
  • 1

1
2 3 4 5 6