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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Why are DNA samples stored as biochemical samples and not 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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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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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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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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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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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 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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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 min to 2 hr depending on ...
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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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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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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 ...
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Is there a newer/better book than Genome-Scale Algorithm Design available? It's from 2015

I'm considering buying the book "Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing" by Veli Mäkinnen and others. However, as this book was ...
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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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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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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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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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Can DNA barcoding be employed to determine the order of an unidentified haematophagous parasite?

Given: a specimen of an unidentified, highly adapted, haematophagous parasite, perhaps a species nova, contaminated with mammal blood and tissue. DNA barcoding is readily used to identify cryptic ...
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What is limiting the accuracy of genome sequencing today?

What are the current limiting factors of genome sequencing accuracy? By accuracy I mean a closeness relation between the sequenced genome and the finally assembled (I am not sure whether there is a ...
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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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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 there any way to identify if chromosomes are inherited from the same parent?

I'm a PhD student in bioinformatics working on genomic data, and I was wondering: If I have access to a person's chromosomes, is there an assay that can determine that two chromosomes come from the ...
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What is the typical arrangement of amplified genes in archaea genome?

I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view. It seems not so difficult to understand, ...
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How are gene and DNA linked in this file?

So I am preparing some documents about Sar-Cov2 and I wanted to illustrate the "definition" of the virus with the DNA sequence. I found this sequence in GenBank. Now I think I need an ...
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why are dizygotic twins genetically dissimilar

I am a high school student and I am a little confused in a topic related to dizygotic twins, I get to know that dizygotic twins are genetically dissimilar because they are formed as a result of two ...
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Why do we use word prime with base pairing in DNA such as 5-3 prime.. prime stand for? [duplicate]

I was reading base pairing sequence in DNA and found 5-3 direction but my question is why we are using word prime with 5 or 3 such as 5 prime 3prime. Prime stand for?
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Why aren't there any competing biologies on Earth?

Why aren't there any competing biologies on Earth? I read sci-books about life based on silicon and I've read an article that said that other structures than DNA can encode genetic information. So ...
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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 ...
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Are there any barriers to telomere sequencing other than length?

In the comments to an answer on this question, it was noted that long read sequencing methods (e.g., from PacBio or Oxford Nanopore) have largely eliminated repeat-based assembly problems for bacteria....
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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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Are there any animals whose genome haven't been sequenced yet? [closed]

I referred to a few websites and it seems like almost every animal's genome has been sequenced. However, are there any animals that haven't yet been sequenced? If so, can you provide the list here or ...
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DNA complementarity against reverse complementarity [duplicate]

I am sorry to bother with this question (i study genetics for about few hours, because I need to understand my data) and I am really confused about these two terms, because I dont know if the books ...
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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 ...
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Population Genetics Using WGS: How do I know when I have enough individuals?

I am having a difficult time finding information about a minimum threshold for number of individuals to use in wgs pop gen analyses. Are there software or formulas/theory available to determine what ...
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Predicting how proteins will be cleaved

Is it possible to predict how proteins coded from mRNA will be cleaved? The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you ...
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What are the advantages of long read sequencing for cancer oncogenomic research?

Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
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Poly-G tails in NovaSeq Paired-end sequencing from museum samples

I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years. The DNA I'm analysing has been sequenced by ...
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2 votes
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How to identify the subspecies/breed of a bee

I have been a beekeeper for a number of years and originally obtained my first colonies from a guy in my neighbourhood. However, when I sell bees to someone else, they typically ask what species of ...
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How long does foreign DNA stay intact in human blood?

How aggressively is foreign DNA in blood targeted and degraded by the human body? I am asking because we have a metagenomics project where we want to detect parasite DNA in the human blood. The ...
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Genome-wide association study (GWAS) search engine?

I am not a biologist and came across the term genome-wide association study or 'GWAS' for the first time today. Now I would like to see if there is a GWAS on the particular condition I am interested ...
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Looking for study/genome data for HIV in different organs

I am looking for a research study or data base that has HIV genome data available in fasta or similar format. Specifically I need genome data of HIV taken from different organs in the same subject. I ...
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Multiple clones Sanger sequencing analysis

I am doing a 96-well arrayed cloning. I have done Gibson, transformations and minipreps in a 96-well format, then sent out the plate for sequencing. Normally, I sequence 3-4 clones and check if 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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DNA extraction kit for microbial mats, rocks, and soil in a remote area

I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For ...
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Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?

I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed ...
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?

I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
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Which was the first DNA-based genome to be sequenced?

The Wikipedia article on phi X 174 states that: The phi X 174 (or φX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be ...
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Polymerase Chain Reaction Specifics

While going over PCR in my biology lecture this week I have come across a few questions I have about this process. First, since PCR focuses on trying to replicate a specific targeted DNA sequence many ...
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Why can DNA tests with mixed DNA of several people not be used to detect a criminal in a database?

Scenario: Two males attack another pair of two males with a weapon. The attackers are fought off and the weapon remains. Why does the police require DNA samples of the two who have been attacked to be ...
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