Questions tagged [dna-sequencing]

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

Filter by
Sorted by
Tagged with
-1
votes
1answer
32 views

How to find the origin of each Single Nucleotide Variants (SNV) in child when having variant call data for both parents?

I am working with a trio (Mom, Dad, Child). I have variant call data for all three. Now I want to know each SNV in the child comes from which parent? Is there any tool that could help me to achieve ...
1
vote
1answer
92 views

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 ...
0
votes
0answers
4 views

“How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?” [migrated]

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
0
votes
0answers
23 views

Why has interest in haplotype blocks waned over the decade?

I looked up haplotype blocks in Google Scholar, and the results returned by its algorithm show that almost all the relevant articles were published between 2001 and 2009. Plus, there was almost ...
1
vote
1answer
30 views

Help Finding Specific BlaZ Gene Type Sequences on Genbank

I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
47
votes
4answers
7k views

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. ...
3
votes
1answer
41 views

Is this basic gene diagram correctly labeled?

I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...
0
votes
1answer
25 views

16S sequencing: pooled or individual samples?

I am planning to run 16S sequencing on a set of individuals to explore microbial diversity. The question I am facing is: should I sequence them individually or I pool them (for example 5 individuals = ...
18
votes
2answers
12k views

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 ...
2
votes
1answer
7k views

Why is only one primer used for DNA sequencing instead of two?

I understand that PCR uses two primers that anneal to the two ssDNA's in order to exponentially amplify a DNA and that Sanger sequencing uses only one primer because a sequence can be determined with ...
1
vote
0answers
20 views

How to determine which allele GRCh37 has?

is there a website where I can search GRCh37 by location or rs IDs, to determine which allele it has at a specific location? I think http://grch37.ensembl.org/ might be the answer to my question, but ...
1
vote
1answer
47 views

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 ...
0
votes
0answers
18 views

identificaation of the correct fragments with desired nucleotide sequences using probes

in making of rDNA, my text book has a point that is written above(the question). what i don't get is if we already know what the nucleotide sequence is why do we need to take out the gene having the ...
7
votes
4answers
296 views

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 ...
4
votes
2answers
432 views

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 ...
9
votes
1answer
2k views

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 ...
0
votes
2answers
45 views

How can DNA replication result in hair pin structures?

My professor said that one of the reasons SSB proteins are so important was to prevent the formation of hair pin structures, I can't see how or why DNA would form hairpin structures and there's not ...
0
votes
1answer
80 views

Design primers for PCR from given DNA sequence

Given the sequence: 5’-ACTGACTATGTAGAA………GGCCCTAAGGGCCAA-3’ (1) You wish to do PCR of this dsDNA to add “overhangs” on the ends of it. On the 5’ end of you will put the restriction site for ...
0
votes
1answer
38 views

Are the alleles that code for the same phenotype all the same exact sequence?

The idea that you can be homozygous for a gene means that there are limited options or alleles , correct ? My question is, if the mom has the allele b which codes for a blue eye, and the dad has an ...
1
vote
1answer
28 views

How do I interpret SNP nomenclature?

I am combing through my 23 & me raw data and I am a little confused on SNP terminology. I am using NCBI's genome browser and SNP database. As an example we can all follow here is a link to a ...
6
votes
1answer
111 views

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, ...
0
votes
1answer
50 views

How to find the enhancer region of a specific gene?

I am new to these concepts in biology and need some help understanding. My main concern is how to find the enhancer of my gene of interest, specifically the sequence of the enhancer. I am working on a ...
1
vote
1answer
44 views

Could tumor cells have normal genomic profiles?

I have thawed primary tumor cells and performed FACS. They were EpCAM positive cells. Then, I expanded them as organoids in 3D and did another FACS analysis. Again, they were EpCAM positive. I also ...
4
votes
3answers
5k views

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 ...
0
votes
0answers
15 views

Why are ligases added with the target sequence in sequencing by hybridisation (SBH)?

I understand that labelled n-mer probes in arrays hybridize with complementary sequences in the target DNA, but I don't know what the role of ligase is in the SBH process. Is it involved in the ...
2
votes
2answers
210 views

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-...
1
vote
0answers
33 views

Hardy–Weinberg equilibrium for SNPs

I have a SNP stats file structure, which contains all information about genotypes and imputed SNP/INDEL imputation qualities, allele frequencies and minor allele assignment. ...
1
vote
1answer
74 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 ...
0
votes
0answers
36 views

Which sample type is more proper for whole genome sequencing in AML patients? Peripheral blood or bone marrow?

I intend to perform whole genome sequencing in AML patients in order to find genomic abnormalities, particularly translocation and gene fusions. However, I am not sure whether it is better to obtain ...
0
votes
0answers
11 views

Any good mitochondrial studies of chimpanzee (or other primate) bands' (groups) female line diversity?

I'm recalling, perhaps incorrectly, that chimps are closest to humans. In theory, we have evolved from similar social groupings. Are there any studies on the diversity of ancestors (mitochondria) ...
0
votes
2answers
98 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 ...
6
votes
3answers
209 views

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 ...
3
votes
1answer
76 views

How much variation in the human genome for humans

We are currently learning about the Human Genome Project in high school biology. Wouldn't the human genome that was mapped be different from, say, mine if it was mapped? How much variation is there ...
2
votes
1answer
66 views

Taq Polymerase's stability at high temperature

I was asked a question as to what is so special with Taq Polymerase that makes it quite stable at high temperatures though its functioning is the same as other DNA polymerases like that of mesophiles. ...
2
votes
2answers
3k views

Do plants have distinctive DNA genomes from each other like humans do?

Can exact same species of plant have a distinct genome from others of same exact species growing nearby or in a different place/country etc. ? Can a leaf be traced to the the exact plant based on DNA ...
0
votes
0answers
22 views

Assessing in soil biodiversity of arid area of US

I am considering assessing the microbial biodiversity (using metagenomics) in the soil of an arid area of Utah (Hanksville) that has dinosaur and other fossil remains. 1) Could it be argued that ...
3
votes
2answers
85 views

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 ...
0
votes
2answers
26 views

What's the difference between the terms “gene map” and “genome”?

It seems some sites arbitrarily restrict "gene map" to only a single chromosome, but others don't. Supposing we don't restrict it to just a single chromosome, is it different from "genome"? Are these ...
2
votes
2answers
124 views

Can 1.5 gigabytes encoded in the human genome really account for the complexity of a human being?

I read the human genome is 1.5 gigabytes in size. Thats actually not a lot; Photoshop probably takes more space. Mac OS takes 10+ gigabytes of space. Also, the genome is 1.5 gigabytes when counting ...
2
votes
0answers
29 views

What does the final (Illumina) RNA-seq library contain? ss cdNA or ds cDNA?

I guess the oligos on Illumina's flow cell only hybridize to to single-stranded cDNAs (sscDNA). However, when I read the TruSeq protocol (googled: TruSeq® RNASample Preparation v2 Guide) at the PCR ...
1
vote
3answers
281 views

How to get phased haplotype from vcf file?

Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased ...
1
vote
0answers
26 views

Single-cell ATAC seq arrays

As part of a data analysis project, I encountered two kinds of single-cell assays for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial ...
-4
votes
1answer
46 views

In a Chromosome, 2 nm is the length of what?

this figure comes from the nature 2 nm at the top right hand corner is the length of what?
0
votes
1answer
23 views

How DNA probe binds

I am studying about southern hybridization now and I've a doubt.After the DNA has been fragmented using restriction enzymes and obtained on nitrocellulose blot , it is still double stranded (the ...
2
votes
3answers
813 views

What is a sequencing artifact?

I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?
1
vote
1answer
56 views

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 ...
1
vote
1answer
92 views

If some humans inherited 3% of Neanderthal DNA, why are we 99.9% same genome? [duplicate]

Many sources say that humans are 99.5 to 99.9 percent the same. Also some sources state that some humans have 3.4% Neanderthal DNA and some don't share those genes. Why is that?
5
votes
1answer
6k views

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?
1
vote
1answer
176 views

Why are two forward and reverse priming sites depicted here? what do they do?

This question is in regard to the baculovirus expression system. (source: amsbio.com) Why do we need to generate primers for the polyhedrin promoter and the baculovirus? Primers are needed to ...
0
votes
1answer
34 views

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 ...

1
2 3 4 5
7