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Questions tagged [dna-sequencing]

Technique(s) by which the sequence of DNA is obtained. The principles are similar for RNA-sequencing.

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What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
Arjun Devdas's user avatar
6 votes
3 answers
303 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: how ...
hello_there_andy's user avatar
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Results of a complete DNA sequencing - are they 100% reusable?

Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)? After that is done, it the complete genome can be stored and once the new genes (and their ...
Mitten's user avatar
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Understanding the strategy of Sanger DNA sequencing

The Sanger sequencing method creates large numbers of sequences of all possible lengths, ending with a specific nucleotide, by terminating with a tagged (fluorescent) nucleotide at the end. But if ...
user9807's user avatar
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4 answers
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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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What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
sharptooth's user avatar
11 votes
3 answers
12k views

What is the strand specificity of a reference genome?

It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. So here's ...
FoldedChromatin's user avatar
10 votes
2 answers
25k views

What is the difference between SOLiD, 454, and Illumina next-gen sequencing?

I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
MattDMo's user avatar
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Finding proteins in DNA sequence

I have to do a task for a university task and I need to understand some things before figuring out how to do it. The task is the following: Find matches of known proteins (DNA-PolyI,II,III) to the ...
atmosx's user avatar
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7 votes
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introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
masfenix's user avatar
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DNA as a digital storage medium; sequences algorithmically avoided for safety reasons (or should be)?

Safety for the environment is probably implicit here as well, but the focus should be on the people who may come in contact with large amounts of synthetic DNA used to encode information as a data ...
uhoh's user avatar
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What are the limitations of commercial-grade DNA genotyping compared to full sequencing?

I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what ...
Alex Stone's user avatar
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301 views

Sequencing from PCR

As far as I understand it, PCR can be used to make many copies of one gene. My question is, is it possible to sequence DNA after PCR and is it easier than sequencing it via other methods. If it is ...
ohblahitsme's user avatar
6 votes
1 answer
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Why is it harder to sequence plant genomes than animal genomes?

Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory ...
Stacked's user avatar
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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 ...
Snake's user avatar
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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 ...
Steve Crawford's user avatar
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2 answers
150 views

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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In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
Tobia Tesan's user avatar
3 votes
1 answer
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What evidence is there that common PCR DNA purification kits can isolate DNA from pathogens engulfed in macrophages?

I have previously asked a more general question about how PCR sequencing reaches all possible DNA targets here. I want to ask more specifically now: what evidence is there that common PCR DNA ...
B M's user avatar
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1 answer
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What does genetically tractable strain mean?

I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this ...
Manuela's user avatar
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What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
dresden's user avatar
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1 answer
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Transcription rate expressed in microarray per hour

This article gives measurement of transcription rate and the unit they're using is microarray per hour. For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...
Remi.b's user avatar
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Don't the radioactive labeled molecules of dNTPs or DNA harm themselves or their surroundings?

I'm reading some papers for the first generation sequencing methods and some earlier than them, like Ray's Wu first time DNA sequencing from a λ phage virus cohesive 5' ends. Ray Wu, like Maxam-...
F.N's user avatar
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1 answer
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Why does one combine PCR and cloning as ways for amplification of sequences?

Why does one combine PCR and cloning as ways for amplification of sequences? Don't they produce the same result? I was reading the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864885/ and got ...
Cindy Almighty's user avatar
2 votes
2 answers
199 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?
Emil_Longshore's user avatar
2 votes
2 answers
621 views

Why do many DNA solutions contain additional compounds?

DNA solubility data in only water is scarce. A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple ...
James's user avatar
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2 votes
1 answer
114 views

Significance of the resequencing of the chimpanzee genome

Introductory remark: I am not a biologist, but a somewhat knowledgeable layperson. I have been told that sequencing of chimpanzee DNA until recently has been done almost exclusively using human DNA ...
itpastorn's user avatar
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2 votes
2 answers
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Help reading chromatogram

A genetic variation is found in this chromatogram: It says that the "reference sequence" is the top line and that I can use the general genetic code to find the reading frame. I can see that there ...
Paze's user avatar
  • 1,381
2 votes
1 answer
96 views

How much of my ancestry will match with my brother?

Recently, my brother (full sibling) got his ancestry checked from MyHeritageDNA. They have a similar service like 23 and me and I've found out that both companies are offering the basic service almost ...
Farhan's user avatar
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2 votes
2 answers
191 views

Do eukaryote cells contain DNA that isn't part of a chromosome or located in the mitochondria?

I specify eukaryote in the title, but I'm also interested if this question isn't applicable to eukaryote cells in general but is to humans. I was reading "RNA-seq: An assessment of technical ...
HBeel's user avatar
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1 answer
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How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
biogirl's user avatar
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What good is the MinION?

This year, Oxford Nanopore MinION has been shipped to some researchers for testing. The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research "...
Superbest's user avatar
  • 4,520
1 vote
1 answer
997 views

What is the difference between 4th generation sequencing and NGS?

The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference ...
James's user avatar
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0 votes
1 answer
61 views

Can contaminants in the DNA extract disturb the sequencing?

I'm having troubles with some DNA extractions. The yields are much lower than expected, and the Nanodrop spectrophotometer is showing quite a bit of contamination through the 260/230 ratios (see table ...
Joel's user avatar
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1 answer
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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 ...
Ganon's user avatar
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0 votes
1 answer
127 views

X-recessive disorders and genetic markers

Please observe the following pedigree of a family with a x-recessive disease (bleeder disease). The A's are genetic markers so close to the disease gene that recombination is negligible. I ...
Paze's user avatar
  • 1,381
0 votes
1 answer
133 views

Simplest Biological Organism? [duplicate]

What is the simplest biological organism from which a DNA sample has been or could be obtained? Could the resulting DNA be processed and examined in such a way that the resulting information would ...
RandomDSdevel's user avatar
-1 votes
1 answer
72 views

What can you learn about someone's mother and father by examining their DNA?

Disclaimer: I ask this question from the position of having paid absolutely no attention throughout school/highschool science classes. I am incredibly ignorant, but I don't know how to find the answer ...
TheIronKnuckle's user avatar
-1 votes
2 answers
131 views

DNA described somewhere?

This is not purely biological question but how do the companies making DNA analysis know what your DNA means? Is there some database describing human DNA? I watched some documents about DNA, gene ...
eXPRESS's user avatar
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