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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How to falsify claim that 2 samples are from different individuals?
Given 2 sealed, air-tight vials1 containing approximately 200 grams each of dried mammal blood. Task is to prove they are (or are not) from the same individual.
What steps would you take?
Note:
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Targeted gene sequencing and specialist analysis compared to WGS and DYI searches
There seem to be a lot of "genetic consulting" services that focus on things like cancer, with a modus operandi of:
Do targeted gene sequencing (usually on a few tumor suppressor genes ...
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Identification of Secondary metabolites gene clusters in fungi
I am trying to identify secondary metabolites gene clusters specifically PKS from endophytes through PCR then sanger sequencing. Are there set of specific primers available or do I have to design my ...
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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 ...
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Is UMI necessary when analyzing samples from Formalin-Fixed Paraffin-Embedded tissues?
We have FFPE-tissues we would like to use for a sequencing run. we think we can get enough biological material, so the amount of RNA shouldn't be an issue, but we're not sure.
A unique molecular ...
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Sequencing a PCR product with no band
I did a PCR that successfully showed the appropriate bands one time, but when I tried to re-do the same PCR just at a larger quantity to send for Sanger sequencing, very faint or no bands were seen. ...
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How does one determine what sequencing coverage/depth to use?
In the context of rare diseases, what sequencing coverage will be sufficient to detect the mutated loci (for eg. SMN1, SMN2 CNVs, gene SNPS, INDELs etc) ? How does this relate to statistics and how ...
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Asymmetric sequencing | Can you sequence 250 bases on Illumina Novaseq S4 (read 2)?
I would like to sequence 250 bases on Illumina Novaseq S4 on read 2.
Kits of illumina come in the following sizes: https://emea.illumina.com/systems/sequencing-platforms/novaseq/specifications.html
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Overlapping annotated regions among repetitive families of human genome
I am studying the repetitive elements in the human genome and I have come to know that some genomic locations are not uniquely described by a single repeat family. What's behind this uncertainty? Does ...
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What exactly is "Whole-genome sequencing"?
Newbie question: For few years I have seen news like “Whole-genome sequencing” is now under $1000 etc. I believed that this means all the base pairs of all chromatids in a single cell are identified ...
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How are probes in capture sequencing synthesized?
In capture sequencing it is common practice to use a panel containing ~10,000 probes. How are these DNA molecules synthesized? I imagine that there is a way to do this in parallel, but I haven't been ...
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How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?
I have two datasets, from different sources, that I need to compare.
The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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What is the expected result when using Sanger Sequencing for Bisulfite analysis on an unmethylated CpG?
Hello fellow molecular biologists!
I'm currently starting out doing a lot of Bisulfite Sequencing and as COBRA is not sufficiently working on my sequence, I do Sanger Sequencing instead, as suggested ...
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What is the function of PCR in the whole genome sequencing?
Whole genome sequencing (WGS) method is using PCR in one of their steps. In the following page from the CDC, we find this diagram:
It says that the PCR is needed to "make copies of each DNA"...
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A DNA extraction protocol that is equipment-less for bacterial metagenomes?
I am going into the field soon to sample a very remote environment. For reasons that are unimportant here, I would like to extract bacterial DNA from these samples in the field.
I will have access to ...
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Is there a word to describe a sample of DNA that can be sequenced?
This is a question about terminology. I want to know if there is a word that is used to describe a sample as "able to be sequenced".
My rough guess would be "sequencable". But that ...
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Is there a term for a sequence of genomes for a family?
Suppose that I am following how a "familial" genome changes throughout generations. That is, I have the genome of a grandmother, father, and daughter, and my objective is to see how the ...
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How can we create a living dinosaur using DNA technology?
I'm wondering what would we need to do to create a living dinosaur using DNA technology? If it is not possible with current technology, will it ever be feasible?
In the movie Jurassic Park, ...
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How to generate PDB file for custom DNA squence(10 base pairs)
I am trying to study docking of drug-DNA interaction and for that I need PDB file.
How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)?
I will really appreciate if you can ...
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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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Does the cell have a mechanism to determine DNA sequence from protein?
Something like a reverse genetic code.
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Does an ORF need a stop codon?
I try to read ORFs from a gene sequence but I am not sure how to interpret a sequence with a start codon but no stop codon. Imagining I have a gene sequence like the following:
...
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Why are DNA samples stored as biochemical samples and not as binary data?
Why are DNA samples stored in cryogenic conditions as biological (or bio-chemical) samples and not as binary data streams of nucleotide sequences in a hard disk or tape drive?
A few reasons I can ...
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Is double-stranded DNA denatured to single-stranded DNA in retorted canned tuna?
A PCR reaction has a cycle of about 55°C annealing, 72°C extension and 95°C denaturing with short time spans. Retorting canned tuna heats the tuna to 115°C to 121°C for 30 minutes to 2 hours depending ...
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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 ...
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What does "run" mean in DNA sequencing?
In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the DNA sequencing:
In reality, most nuclear genomes are a mixture of unique sequences and short and long ...
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How can "position" be measure by bp unit?
In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the CNV:
Whole-genome re-sequencing is fast becoming the norm in the field of human comparative genomics. ...
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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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How do we know Denisovans had 46 Chromosomes
What allows sequencers to conclude that Denisovans had 46 chromosomes rather than merely knowing Denisovans had the crossover material arranged in 48 or say 44 chromosomes?
See http://genetics....
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What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci?
The article about "rapture sequencing" found
here says:
"This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses ...
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What does it mean to collapse heterozygous alleles?
I am a bioinformatics rookie. I read a paper, it said:
existing algorithms either collapse heterozygous alleles into one
consensus copy or fail to cleanly separate the haplotypes to produce
high-...
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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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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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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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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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How sensitive are "cheap" genetic sequencers these days?
It is in the news that tomatoes with a Sl7-DR2 knockout are being trialed in England, with a view to being commercially grown and available to consumers. While this would be legal in England, it ...
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What results would come from DNA analysis of several different types of DNA mixed together?
By "types," I mean several different species of animals. If, post extraction, the pure, isolated DNA of several different animals were mixed together and run through DNA analysis, I know the ...
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Hierarchial and shotgun sequencing vs Massively Parallel Sequencing
Why is the cloning step unnecessary prior to sequencing with massively parallel sequencing (MPS; Illumina or similar technologies), when it is necessary for hierarchical and shotgun sequencing?
I know ...
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What were the challenges to sequencing the last 8% of the human genome that took 20 years to overcome and how was this done? (T2T Consortium)
CNN's March 31, 2022 article Scientists sequence the complete human genome for the first time says:
In 2003, the Human Genome Project made history when it sequenced 92% of the human genome. But for ...
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How many MAOA alleles are there?
The question is about the human gene MAOA.
I've seen MAOA-H and MAOA-L mentioned in papers.
The page https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000189221;r=X:43654907-43746824 ...
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Do 0.2 vs 0.5 ml epitubes require different PCR machines, incubators, etc?
Eppendorf themselves and many other companies list on their website two above mentioned sizes of "PCR tubes". As I understand 0.2 ml is by far more widespread and "standard" for ...
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Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?
My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from ...
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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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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 ...
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What is the shortest read length achievable using Oxford Nanopore sequencers?
Is there a lower limit, in terms of read length, one could expect from sequencing DNA on Oxford Nanopore devices?
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Complete human rDNA sequence
I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find ...
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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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Gene Sequencing [closed]
The human genome project took an effort of around 15 years, billions of dollars and thousands of scientists working together.
So how is that the genetic sequencing of covid variants could be done at ...
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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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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 ...