Questions tagged [genomics]

The study of genomes, the entire set of genes in an organism.

Filter by
Sorted by
Tagged with
-1
votes
1answer
24 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 ...
0
votes
0answers
4 views

“How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?” [migrated]

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
0
votes
1answer
40 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).
2
votes
0answers
40 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 ...
3
votes
1answer
41 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 ...
1
vote
2answers
89 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 ...
0
votes
1answer
41 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 ...
4
votes
2answers
432 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 ...
0
votes
3answers
113 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 ...
0
votes
1answer
27 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 ...
2
votes
3answers
71 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 ...
-1
votes
1answer
56 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 ...
0
votes
2answers
26 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 ...
0
votes
0answers
21 views

LacZ gene presence in E.coli strain with Blue-White Screening

I'm not quite familiar with the concept as described in the title. Lets say one wants to use an E.coli strain as a host for a pUC-vector and you want to use Blue-White Screening. What should be the ...
1
vote
1answer
243 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?
1
vote
0answers
26 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 ...
3
votes
0answers
66 views

Is mating between human and non-human primates theoretically possible?

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 ...
-1
votes
1answer
31 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 ...
0
votes
1answer
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?
1
vote
1answer
33 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 ...
-1
votes
1answer
34 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?
1
vote
1answer
46 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 "...
0
votes
1answer
47 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 ...
1
vote
2answers
109 views

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 ...
1
vote
0answers
15 views

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 (...
0
votes
1answer
34 views

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 ...
3
votes
1answer
95 views

Is there any independent non-DNA based information system in the cell

The information in protein is not neccessarily independent of the genome as the information of amino-acid sequence comes directly from the genome. The process of post-translational modification may ...
1
vote
1answer
117 views

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 ...
1
vote
0answers
49 views

Why more than one chromosome in an organism?

Why not one chromosome to house genome in organisms but multiple? Is it for epigenomic purposes?
0
votes
1answer
24 views

What are low-accumulating genotypes? [closed]

What are low-accumulating genotypes? And how does it differ from high-accumulating genotypes?
-2
votes
1answer
130 views

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-...
1
vote
2answers
136 views

Is it possible to deduce facts about a person's parents just by studying his/her genome?

As an example, suppose Anne had abusive parents. Is it theoretically possible to deduce this from her genome even if she didn't inherit this quality (of being an abusive parent)?
4
votes
0answers
92 views

Realistic Application of CRISPR in Human Disorders

Human trials recently began to use the genome editing technology CRISPR to treat sickle cell anemia using edited stem cells. Sickle cell anemia is caused by a single DNA Mutation, and is also a ...
2
votes
1answer
90 views

an umbrella term for homeolog and ohnolog?

Is there a word that refer to homologous chromosomes within a polyploid species? If I have AABB species, what is A to B? The words "homeolog" and "ohnolog" are reserved for the cases if the ...
10
votes
3answers
855 views

Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

One of the major results of the Human Genome Project (HGP) was that humans have far fewer separate genes than previously thought. From a 2004 article about the HGP: Francis S. Collins, director of ...
0
votes
1answer
254 views

Is transition more common than transversion during the evolution of duplicated genes?

Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G &...
3
votes
0answers
114 views

Construct picture of person's face from DNA

Would it be possible to construct a picture of a person's face from his/her DNA?
3
votes
1answer
101 views

Why is GenBank growth slowing down?

https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are ...
4
votes
1answer
903 views

What is structural RNA?

In genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Fungi/Saccharomyces_cerevisiae_uid128/) there are an archive .frn (nucleotide sequences of structural RNAs in fasta format), and I ...
2
votes
1answer
58 views

What does “This variant falls on 11 transcripts in 3 genes” mean in the output from GnomAD?

The gnomAD browser provides information on variants of genes (in this link, for the SAMD11 gene.) The report on a particular variant, like this one, includes the information in the header that says ...
1
vote
2answers
38 views

Pyura DNA extraction

I'm am struggling with genomic DNA extraction from different samples of Pyura chilensis; the DNA is degraded as can be seen on the gel. We've always used GeneJET Genomic DNA purification Kit (by ...
-2
votes
1answer
38 views

Can you do DNA seq with Microarray? [closed]

Is it possible to do the entire DNA sequencing with Microarray or would you have to use Sanger or NGS methods for that?
-1
votes
2answers
50 views

filtering variant list according to target regions

I have a variant list in VCF file for a particular disease, I want to filter these variants according to exonic regions in a BED file using a Perl script. How I do this?
1
vote
0answers
32 views

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 ...
0
votes
1answer
59 views

What is a genome? [closed]

By genome do we mean a consensus sequence of DNA or a set of sequences that ideally captures all possible variations?
2
votes
0answers
38 views

How much DNA does a species lose after post-polyploidization genome downsizing?

After whole genome duplication, diploidization takes place, right? A lot of changings in gene organization and expression involving genetic and epigenetic mechanisms (translocations, transpositions, ...
1
vote
1answer
92 views

Gene copies vs. gene paralogs - what's the difference?

I'm trying to get into the theory and practice of gene copy number variation (CNV) analysis, but there is something basic confusing me, which I couldn't yet figure out. Sorry if this is a dumb/trivial ...
0
votes
1answer
24 views

tissue-specific expression of homolog genes

Two or more genes are homolog if thay have similar sequences. homolog sequences between species are called orthologs (caused by speciation events) and homolog sequences in an species are called ...
0
votes
1answer
110 views

Finding phylogenetic distance between sequences?

I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
3
votes
0answers
70 views

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 ...

1
2 3 4 5