If you are looking for information on Coronaviruses, we have prepared this FAQ with information on what is on topic on this site and links to some reputable external resources.

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
0
votes
1answer
46 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
0answers
14 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 ...
1
vote
0answers
28 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
71 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
35 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
9 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) ...
1
vote
1answer
42 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 ...
0
votes
1answer
43 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 ...
0
votes
2answers
71 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 ...
3
votes
1answer
74 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
63 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. ...
0
votes
0answers
20 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 ...
0
votes
2answers
24 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 ...
3
votes
2answers
77 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 ...
2
votes
2answers
118 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
28 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
0answers
23 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
42 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
21 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 ...
4
votes
0answers
87 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, ...
6
votes
3answers
164 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 ...
2
votes
3answers
575 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
54 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
87 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?
0
votes
1answer
31 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 ...
0
votes
1answer
38 views

Are the Fastq files content is truly random

I'm building a system to generate fastq files as they are being output from HiSeq 3000 and HiSeq 4000. This will serve us to test our internal systems with some gold standards. As we are working with ...
2
votes
1answer
83 views

How many palindromic sequences in human genome?

I'm writing an article on palindromes (the words) and I wanted to mention the existence of palindromic gene sequences. Roughly how many palindromes exist in the human genome? I understand the number ...
0
votes
0answers
66 views

Why do genetic testing companies (FTDNA,AncestryDNA,23andme) express DNA shared in centimorgans (cM) instead of in number of base pairs or in percent?

Expressing DNA shared in number of base pairs or in percent of total genome would be so much simpler and easier to understand for the customers. .
2
votes
1answer
97 views

A cure for radiation exposure?

Some of the greatest inventions of my lifetime have been from looking at nature and copying. I found out tadigrades in outer space have the ability to repair their own DNA when exposed to radiation ...
1
vote
1answer
49 views

Do we posses technology to rebuild sequenced DNA? [closed]

Is there existing technology that would allow to rebuild DNA molecule from a digital file storing sequenced DNA? If not, does there at least exist theory explaining how such device could be built?
2
votes
1answer
104 views

Must I HPLC-purify my PCR Primers for amplicon sequencing with PacBio SMRT?

I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers). The resulting ...
2
votes
2answers
94 views

Meaning of Phred score - probability of base calling error

I learned that Phred quality scores are logarithmically linked to error probabilities. For example, if Phred assigns a quality score of 10 to a base, the chances that this base is called incorrectly ...
0
votes
1answer
80 views

How does Sanger sequencing resolve two bands with equal size? [closed]

In Sanger sequencing, how can we read the sequence if we have 2 bands with the same size?
2
votes
0answers
65 views

What are haplotype blocks and what is the effect of hybridization on these?

In this PDF, there is a quick definition of haplotype blocks. A haplotype block is a set of closely linked alleles/markers on a chromosome that, over evolutionary time, tend to be inherited ...
1
vote
2answers
136 views

Is it possible to deduce facts about a person's parents just by studying his/her genome?

As an example, suppose Anne had abusive parents. Is it theoretically possible to deduce this from her genome even if she didn't inherit this quality (of being an abusive parent)?
2
votes
1answer
76 views

How much of my ancestry will match with my brother?

Recently, my brother (full sibling) got his ancestry checked from MyHeritageDNA. They have a similar service like 23 and me and I've found out that both companies are offering the basic service almost ...
1
vote
1answer
45 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
1answer
18 views

denovo 2Gb whole genome sequencing on a small sequencer

What are the limitations of using Illumina's smaller sequencers (e.g., iSeq100, miniSeq) to do de novo whole genome sequencing on an organism with a larger genome (~2Gb)? Naively, it seems even if I ...
1
vote
1answer
273 views

What experiment for first time showed DNA is anti-parallel? [closed]

Scientists how to prove DNA is anti-parallel?
0
votes
0answers
31 views

Any examples of a group of micro-organism that continuously spans two or more species classifications?

Are there any examples of a group of micro-organisms where two different, established species are designated and these two groups meet all aspects of the definition of species (perhaps can not ...
2
votes
0answers
46 views

DNA preservation at room temperature

I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in ...
1
vote
1answer
44 views

Sequencing inaccurate at the primer site

The times I have sent a sample to sequence, both the forward and the reverse primer sites, show high inaccuracy while the rest of the gene is correctly sequenced. Because of this, the sequences of my ...
-1
votes
1answer
40 views

Error frequency of DNA replication without proof reading activity of DNA polymerase?

Different domains of DNA polymerase contain different activity, like 5'->3' polymerisation and 3'->5' proof reading ...
0
votes
1answer
18 views

Isolating a specific gene (specifically TRAV* series of genes) for sequencing

I'm trying to figure out (for pedagogical purposes) the right way to isolate and PCR the regions coding the T-Cell receptor. My understanding is that I would need to use restriction enzymes that ...
1
vote
1answer
67 views

Can supplements affect DNA? (Could 10,000% Methylcobalamin affect MTHFR genotype)

Originally titled "Could B12 supplementation affect dna test results for B12 need?" - B12 just seems like a good example question to frame the more general question of "Can supplements affect DNA?" I ...
2
votes
1answer
36 views

How are fragments isolated during shotgun Sanger sequencing?

For a large genome (say millions of base pairs) -- we split the genome into fragments < 1000bp that are sequenced and can then be put back together computationally. My understanding is you use ...
0
votes
1answer
151 views

Is it possible to re-align of SAM/BAM files?

I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first ...
3
votes
0answers
113 views

Construct picture of person's face from DNA

Would it be possible to construct a picture of a person's face from his/her DNA?
1
vote
1answer
21 views

Is there a biological explanation for a 0.5 difference in allele size with PCR product?

CONTEXT I am currently working on a set of diversity, this diversity in interspecific (within the same genus). I am using SSR markers, the primers were designed on one species and are working really ...
1
vote
0answers
46 views

How diverse are the sperm cells of an individual male due to random mutations?

Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species? For instance would it ...

1
2 3 4 5
7