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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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How do you find the template strand for a sequence where start codon is in both strands?

Maybe I'm missing something very obvious but I can't seem to understand how to find the template strand given a sequence and its complementary strand if both strands contain ATG from 5' -> 3'. ...
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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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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 ...
Assa Yeroslaviz's user avatar
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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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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. ...
Nalonda's user avatar
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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 ...
Loki123's user avatar
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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 ...
bud.dugong's user avatar
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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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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 ...
AVO's user avatar
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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 ...
Peter Wu's user avatar
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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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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 ...
donkey's user avatar
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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 ...
Kevin Bowersox's user avatar
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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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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 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: ...
yemy's user avatar
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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"...
discipulus's user avatar
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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. ...
Ahmed Samir's user avatar
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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 ...
Ahmed Samir's user avatar
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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 ...
Ahmed Samir's user avatar
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1 answer
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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-...
Fan Yang's user avatar
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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 ...
Lord Loh.'s user avatar
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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 ...
FeywildWest's user avatar
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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 ...
George's user avatar
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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 ...
katara 's user avatar
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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 ...
uhoh's user avatar
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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 ...
beardeadclown's user avatar
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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 minutes to 2 hours depending ...
A Old Tuna Guy's user avatar
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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 ...
neurosciencecalc's user avatar
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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 ...
Tarique's user avatar
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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 ...
James's user avatar
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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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2 votes
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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 ...
pans's user avatar
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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 ...
gcorso's user avatar
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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 ...
dnalectronics's user avatar
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589 views

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 ...
ilam engl's user avatar
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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 ...
Serge Stroobandt's user avatar
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1 answer
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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 ...
Frank Hauser's user avatar
9 votes
2 answers
489 views

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 ...
CorinaPlus's user avatar
12 votes
3 answers
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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 ...
ilam engl's user avatar
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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 ...
Whitehot's user avatar
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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, ...
Manuela's user avatar
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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 ...
totalMongot's user avatar
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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 ...
Arun Bhardwaj's user avatar
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2 answers
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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?
Alex's user avatar
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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 ...
TheIronKnuckle's user avatar
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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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