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 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.
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Why are there N's after Sanger sequencing?
After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence. I know the N's mean that the computer can't tell what the base pair is, but why is ...
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Why do restriction enzymes tend to have an even number of bases in their recognition site?
When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases.
I wondered if this was just a co-incidence, so I took the data from this ...
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Why was it so hard to decode the corn genome?
My teachers growing up told me it was impossible to decode the maize genome. But yet its been done.
Why was decoding the genome so significant, and what made it so difficult?
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Why did high A+T content create problems for the Plasmodium falciparum genome project?
The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
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Looking for a cancer drug target database to guide sequencing of patient tumor DNA
I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s ...
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Questions to ask to a panel of people that will be sequenced
Some genes have been shown to be associated with left-handedness.
Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or left-...
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When does BLAST fail to align 2 DNA sequences?
This is an assignment that had confused me for a long time. So I think you guys who study computational biology might be interested. The original question is:
Find the two most similar DNA ...
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Sequencing the genomes of polyploid organisms
I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
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Would it be possible to sequence human DNA from wastewater treatment plants?
I know that there are some efforts from scientists working with bladder cancer to perform liquid biopsy from urine for detection and monitoring of the cancer such as this one.
I've been searching ...
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Is TTGATATAT a gene?
Biologists use the sequence of letters A, C, T and G to model genomes. A gene is a substring of a genome that begins after the three-character ATG and ends before the three-character TAG, TAA, and TGA....
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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 ...
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protocol for pulldown of DNA breakpoints?
Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination ...
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What are the limitations to current nucleotide sequencing technologies?
Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
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Standard practice for generating rarefaction curves from Next Generation Sequencing data
We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database.
To generate a ...
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How can I preserve hair or saliva for future genome sequencing?
Suppose I want to preserve myself so that I can be reproduced as best as possible, in future or be simulated in future. At the moment full human genome sequencing is a bit expensive.
One could get ...
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What is the difference between sequence, reads, and contigs of genetic material?
Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example?
I am new to bioinformatics, and I have not found any conclusive ...
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What's the difference between shotgun sequencing and clone based sequencing?
In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...
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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 ...
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Digital Genomic Footprinting for ENCODE
I'm reading over the ENCODE Nature papers, and one of the papers referred to is "Global mapping of protein-DNA interactions in vivo by digital" by Hesselberth et al[1].
Genomic footprinting is a ...
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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 ...
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If we sequenced the genome of every species, would all phylogenies agree?
The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
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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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Could someone explain the join in the SARS-cov-2 genome at location 13468?
I am having trouble understanding the reference sequence for sars-cov-2, NC_045512.2
Three nucleotides equals one amino acid, right? But the nucleotide at position 13468 seems to be used twice, so ...
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BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:
It looks like it's ...
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Alternate genetic codes in newly sequenced organisms
Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. ...
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Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?
There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it ...
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Can I compare Shannon indices of metagenome gene data?
I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the ...
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What's the use of DNA sequencing results?
Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides.
What's the use of that? It's just a "string" where nucleotides encode ...
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How to clone and sequence a gene transcript of unknown sequence?
How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA ...
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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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What is the difference between sequence alignment and sequence assembly?
I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
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How are whole Haplotypes for Sequencing isolated?
Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered ...
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Limitations of 16S rRNA sequencing
Looking at the microbiome analysis literature there seems to have been a shift away from 16S rRNA sequencing analysis toward shotgun sequencing of the whole genome. While the motivation given is ...
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Looking for a DNA sequence
I am not a biologist. Please pardon me, if my question does not make sense.
I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence ...
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Why are there two abrupt changes in the genome sequencing price curve?
In the price curve of the genome, from NIH:
NIH explained the abrupt drop at 2008 thusly:
beginning in January 2008... the sequencing centers transitioned from Sanger-based (dideoxy chain ...
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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 ...
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What causes skewed lanes in a DNA gel electrophoresis experiment?
In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)?
(These images were samples that I took from an online activity we did for class)...
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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 ...
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Whole Genome Sequencing vs Whole Exome Sequencing
I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:-
I am looking at SNP's and ...
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Mechanics of going from DNA sequence to metabolic network
My apologies for possibly a naive question. I'm a statistics type and have been asked to assist with analysis of metabolic pathways (and networks). However, I would like to have at least a layman's ...
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How can I generate a random DNA sequence?
I've found this paper which involves the construction of 19-bp random DNA sequences, but I don't know enough biology to understand how this method works. Could someone explain it to someone who is ...
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Is there a detectable amount of bacterial DNA in the blood of infected persons?
With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood?
If any is found it is likely not to be very much, and even difficult to distinguish from ...
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ChIP-seq vs ChIP-exo
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.
As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
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What is a genetic marker?
In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and ...
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What percentage of the human genome hasn't been sequenced yet? If percentage estimates aren't precise, why is it difficult to estimate?
What percentage of the human genome hasn't been sequenced yet? I have read different estimates, e.g.:
https://www.genome.gov/human-genome-project/Completion-FAQ (mirror): "In the April 2003 version, ...
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Sequence of ribosomal RNA
Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, ...
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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 ...
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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 ...
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In percentage, how much is the human genome (DNA) similar to the mouse genome?
Some guy argued with me against evolution theory, and he claimed that human and mice share 98% just like human and chimpanzee.
I've tried to search online for a simple and accurate answer, but I ...
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