Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [genomics]

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

0
votes
1answer
13 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
29 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 ...
4
votes
1answer
4k views

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?
-1
votes
1answer
23 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
2answers
60 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
1answer
32 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
45 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
0answers
14 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
28 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
0answers
111 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?
4
votes
0answers
79 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 ...
3
votes
1answer
98 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 ...
0
votes
1answer
105 views

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?
4
votes
2answers
275 views

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 ...
3
votes
1answer
89 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
91 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 ...
5
votes
1answer
7k views

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 ...
0
votes
0answers
30 views

Why don't all protein sequences taken from DNA get synthesized?

Why don't all protein sequences in DNA get synthesized? The genome, and subsequently extracted proteome, is much larger than the collection of proteins for which there is any other experimental ...
1
vote
0answers
43 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?
1
vote
1answer
8k views

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?
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?
0
votes
1answer
133 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 &...
-2
votes
1answer
118 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-...
10
votes
3answers
738 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 ...
1
vote
2answers
122 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)?
2
votes
0answers
54 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 ...
2
votes
1answer
46 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
35 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 ...
3
votes
1answer
3k views

What is pQTL and why do we need eQTL?

eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia). There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly ...
5
votes
3answers
7k views

How many recombination events are there per generation in humans?

I'm looking for a reference that tells me how many recombenation events occur in humans from one generation to the next. Assuming that the human genome is a 3.3 GigaBases long DNA sequence, how many ...
-1
votes
2answers
32 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?
7
votes
1answer
299 views

What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?

The recent news about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but ...
0
votes
2answers
101 views

What is the likelihood of a single human gene to the same gene from the other human?

The human genome comprises 3,234.83 Megabases and contains ~ 19,000 genes. It has been estimated that the genomes of humans are 99.9% identical. How likely is it that any single gene might vary from ...
1
vote
1answer
287 views

What's a structural RNAs?

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
34 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
vote
0answers
30 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
45 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?
1
vote
2answers
66 views

Can PCR duplicates have complementary sequences?

It is common when analyzing paired-end whole-genome shotgun sequencing data to check for and eliminate PCR duplicates. The reasoning is that the probability of sampling a fragment of the genome of the ...
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
74 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
104 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 ...
0
votes
1answer
151 views

Confirming exon shuffling in a gene

I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro ...
-2
votes
2answers
1k views

When is gene density an important parameter in experiments?

As per wikipedia definition, gene density is defined as: "In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in ...
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 ...
3
votes
0answers
63 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 ...
11
votes
3answers
1k views

What distinguishes “coding” from “noncoding” DNA?

I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA". I'm just an interested layperson but I thought all combinations of ...
2
votes
3answers
208 views

Definition of the different DNA regions

Reading from Oshima et al. (2016): We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and ...
7
votes
2answers
3k views

What's the longest transcript known?

What's the longest functional transcript known? I'm wondering about RNA length post splicing, so not including introns.
1
vote
0answers
22 views

Characterising mechanisms responsible for generating structural variants

I have a high-quality set of structural variant breakpoints from tumour/normal WGS data, and I am interested in digging into the various mechanisms that might be involved in each event. There are ...
0
votes
1answer
95 views

Open databases for copy number variations similar to TCGA

The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal ...