Questions tagged [genomics]

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

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69 views

How can one calculate “probability of possessing a ‘perfect’ profile” from “typical optimal genotype frequencies”?

Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper? Paper link here
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Which is a good methodology to find out a domestication process?

I just started with my course in genomics and I'm working with domesticated animals (cows, chickens, pigs, etc) and I would like to know which methodology is better to trace the process of ...
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Why are sushi proteins called “sushi”? What are the origins of this name?

Does anybody know why complement control proteins (also short consensus repeats) are called "sushi" proteins? Is there any special reason for their name?
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246 views

Which are the best programs to analyze circular RNA?

Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have ...
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224 views

Actual determination of the DNA sequence in the shotgun approach?

I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
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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?
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252 views

Example of code with pypgen (python)

I have a VCF file and wish to calculate a few indices of population divergence over a sliding window. I consider using pypgen but the documentation is currently very limited. Can you please give me ...
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2answers
374 views

How to detect Single Nucleotide Variants (SNVs)?

This image is obtained from this paper. The description of this image is as follows:- DNA-sequence reads from a tumor sample are aligned to a reference genome (shown in gray). Single-nucleotide ...
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395 views

Which DNA elements belong to the definition of a gene?

I see a lot of different DNA elements mentioned as part of a gene (talking about eukaryotes): The length of DNA following the promoter is a gene and it contains the recipe for a protein. (video) ...
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270 views

Making Cupriavidus metallidurans in laboratory? [closed]

This is probably a stupid question but would it be possible to 'make' Cupriavidus metallidurans? And if so how? I'am guessing it wouldn't be possible without the use of expensive equipment for genome ...
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1answer
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What is the metagenome like for other classes of animals?

Lately there's been a lot of discussion around the many non-human cells essential to a healthy human body — called the microbiome, or metagenome. Much of this is in the gut microbiome. See this ...
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Possible complications due to gene-therapy?

Edward Lanphier, CEO of Sangamo BioSciences mentions here(https://youtu.be/dJ1B8XnyEnM?t=1215) that scientists can now specifically target cells, change the genome within a cell. Say you want to cure ...
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Excluding the Exon, What Does the Rest of the Genome Do?

The exon is the portion of the genome that encodes protein synthesis, if I understand correctly. But, this exon is apparently less than 5% of the genome. So, what does the rest of the genome do?
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Can different bacteria strains of same species have different genomic sizes?

Can two different strains of a single species have different genomic sizes? I am not asking about plasmid. Can they have different sizes of actual chromosome?
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What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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1answer
509 views

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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can genetic material actually provide a physical description of appearance?

A bodies genetic material provides the blueprint for your appearance. Your predisposition to be tall, freckled, blue eyed and blonde are encoded from birth. However, external and environmental ...
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874 views

Gene configuration : Divergent vs convergent

I start reading a paper where they discuss the effect of the divergent promoter/gene and the convergent promoter/gene on the genetic expression of an organism. So I want to know what is the ...
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4k views

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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What is a topological domain?

I found this definition on Wikipedia, but I didn't quit undestand it : Topologically associating domains (TADs) are genomic regions ("chromosome neighborhoods") used to summarize the three-...
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Are the human genes' promoters all known?

It seems to be a basic question, but I couldn't find a certain answer. The human genome is known for more than a decade, and is available through several data providers as the NCBI etc. For the genes'...
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Why do we need two markers to measure a recombination rate?

In calculating recombination, Why is it necessary to take into account pairs of loci where one marker is heterozygous? Why is it necessary to take into account pairs of loci where both markers are ...
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137 views

Why is a screening process required in selection from a genomic DNA library?

After the process of construction we go for screening process of selecting a recombinant host. Which includes: DNA hybridisation Colony hybridisation Random primer labeling Nucleotide ...
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453 views

Two sets of chromosome and the sequencing output

Humans have two sets of chromosomes that are not connected in each cell. Am I correct? I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some ...
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DNA Sequencing and genotyping [closed]

Before going to the details of the question let me post a few other details- (I posted something similar and got no useful answers-probably because I didn't explain things properly or something else)- ...
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896 views

Sequencing two strands of dna

My background is not genetics. 2.I am not interested in knowing how dna sequencing or genotyping is done. 3. I am interested just in the nature of the results as described here. Now coming to the ...
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Lampreys and the origin of certain brain structures

I'm not sure why, but I'd been under the impression that things like the optic tectum and basal ganglia developed post-2R (the double duplication of the genome ~1/2 Ga). Lampreys (as far as I'm aware)...
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140 views

Alignment of sequenced fragments in Next Generation sequencing (sequence assembly) [closed]

The NGS (Next Generation Sequencing) involves fragmenting the DNA to be sequenced. This is followed by attachment to beads or flow cells and then a localized PCR is conducted. Modified bases are added ...
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3answers
263 views

Genome and Proteome

Due to the dynamism of protein expression, a genome can give rise to different proteomes, but could we say that a proteome comes from different genomes?
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Full Sequence for Plasmid pMG101

I am trying to find the full plasmid sequence for pMG101. I have been looking through other papers that have sequenced this plasmid. The GenBank access numbers I got are the following: AY009372–...
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Quantifying the number of fragments from RAD library

I have a series of single-end reads from a RAD library of 48 uniquely tagged individuals in fastaq format. The data comes from a small MiSeq run. I want to know the number of unique fragments per ...
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175 views

Is DNA sequencing coverage a function of sample purity?

How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?
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1answer
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Calling Alterations in Exome Data

What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer ...
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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?
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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3answers
9k views

How is the size of a gene defined?

Is there an agreed definition as to how many nucleic acid bases constitute a gene? If not, why not? I'm not sure I understand how the exact sizes of genes are defined.
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Perplexing by the way of estimating the shared or different genes between humans and chimps

We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred ...
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Current state of Gene Therapy [closed]

I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood. (i) Are there approaches ...
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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 ...
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2answers
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How do biologists quantify “gene expression” in experiments?

I've read papers which contain statements such as "control of gene expression is critical in biological processes". How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
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What further research can the result of gene variation detection be used for [closed]

We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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459 views

What physical traits are derived from the Neanderthal DNA in human DNA?

Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between Homo sapiens and Neanderthals. Now the Neanderthal looked a bit ...
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235 views

Can both the overlapping genes (in opposite strands) produce proteins?

I have recognized that both the forward and reverse transcripts from a genomic location code for protein products. Both do occur/express in the tissue of interest. In order to eliminate by chance ...
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3k views

How exactly are gaps defined in genomics?

My understanding is that when sequencing a genome, "gaps" refer to fragments which were not sequencing in the sequencer. Is this correctly? What are there other meanings to the term "gap"?
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276 views

How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
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47 views

Genomic distribution of tRNAs in eukaryotes

The title says it all. I'm doing a literature search trying to see what is widely known and/or well established. I've found a couple of mentions that tRNAs are dispersed throughout the entire nuclear ...
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1answer
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Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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376 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...