Questions tagged [genomics]

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

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39 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).
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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Over winding vs under winding of a DNA

DNA supercoiling refers to the over- or under-winding of a DNA strand. Source : DNA supercoil When a relaxed DNA is subjected to bends, or openings of DNA, over winding or unwinding, its base ...
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Topological property of DNA

I was reading a course about DNA Supercoiling, and I stopped at this definition : [...] In the case of DNA, a topological property is one that is not affected by twisting and turning of the DNA ...
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Amount of Heterozygosity

How many loci in the human genome are heterozygous? How about other species? EDIT: I was wondering, considering for example the whole world population, how many of the human genes actually have two ...
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DNA methylation and genome size

Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability ...
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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 ...
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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 ...
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How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here? Binding of the triphosphate ...
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Difference between CDS and cDNA

What is the difference between Coding Sequences (CDS) and cDNA? Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured ...
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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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Are SNPs and alleles the same thing?

It seems to be quite difficult to find an answer to this. Are SNPs the same thing as alleles?
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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?
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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 "...
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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 ...
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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 (...
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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 ...
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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?
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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 ...
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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 ...
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Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling? At present using the DP > 10 and Q > 30 for Variant calling. Is it ok?
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Publicly available resources for learning metagenomics

We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online ...
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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 ...
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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 ...
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What does conditional analysis of a SNP in a GWA study entail?

I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
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Why more than one chromosome in an organism?

Why not one chromosome to house genome in organisms but multiple? Is it for epigenomic purposes?
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What is splice junction pairs?

Splicing is a modification of pre mRNA when all introns are removed and exons are joined. What is a splice junction pair? It is two exons which connected together?
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What are low-accumulating genotypes? [closed]

What are low-accumulating genotypes? And how does it differ from high-accumulating genotypes?
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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 &...
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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-...
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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 ...
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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)?
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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 ...
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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 ...

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