Questions tagged [genomics]
The study of genomes, the DNA complement of organisms.
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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 ...
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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 ...
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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 ...
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Is it possible to find a description of the different columns when exporting data from Yeastmine?
I am trying to export some genomic data from Yeastmine. The webpage lets me select relevant variables from a long list of features and use them to create a table where the different columns correspond ...
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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 ...
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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:
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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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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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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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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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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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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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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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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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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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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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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 ...
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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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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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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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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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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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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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