Questions tagged [dna-sequencing]

Technique(s) by which the sequence of DNA is obtained. The principles are similar for [tag:rna-sequencing].

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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?
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What is the practical use of one's DNA sample?

I have the opportunity to have my whole genome sampled and receive the raw results. What are the practical use I can make of it? I know of companies (23andMe for instance) who will process a sample, ...
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1answer
47 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 ...
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1answer
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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?
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1answer
37 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 ...
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1answer
4k 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?
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1answer
163 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 ...
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1answer
28 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 ...
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1answer
80 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 ...
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1answer
98 views

Does increasing the value of k in k-fold coverage requires more memory?

Study: Here is what is k-fold coverage which is know as sequence coverage. According to this, 2-fold coverage means the whole DNA is sequenced more twice in average. Question: If I have a genome ...
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3answers
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What's the difference between shotgun sequencing and clone based sequencing?

In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...
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1answer
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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 ...
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1answer
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What happens after the purification step in Hi-C sequencing?

I am a statistician reading an article on Hi-C, and I am trying to better understand one of the steps in the DNA isolation and sequencing process. Since I'm a statistician, please try to avoid too ...
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0answers
48 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 ...
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4answers
2k views

If we sequenced the genome of every species, would all phylogenies agree?

The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
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0answers
111 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?
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1answer
75 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 ...
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64 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. .
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1answer
61 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 ...
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1answer
88 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 ...
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1answer
45 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?
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1answer
98 views

Why is GenBank growth slowing down?

https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are ...
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1answer
105 views

Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling? At present using the DP > 10 and Q > 30 for Variant calling. Is it ok?
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1answer
109 views

What is mRNA expression level?

I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.
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What is the structure of DNA during Interphase? Chromatin Fibre or Beads on a string(nucleosomes)?

During Interphase, does DNA predominantly exist as Chromatin Fibre (30nm fibre) or Chromatin/beads on a string structure(10nm) ?
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1answer
71 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 ...
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2answers
57 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 ...
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1answer
56 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?
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2answers
120 views

Sequence of ribosomal RNA

Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, ...
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2answers
1k views

What causes skewed lanes in a DNA gel electrophoresis experiment?

In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)? (These images were samples that I took from an online activity we did for class)...
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0answers
13 views

Translocation and Isolation of Specific Bacterial Codons

I am currently working on a research project in which I am aiming to translocate a gene from a specific bacteria (strain NT-26, an arsenic oxidizing bacterium) into another bacterium. I am doing this ...
2
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1answer
81 views

How does a polymerized TruSeq adapter affect sequencing reads?

I am trying to build a NGS library on enriched DNA (DNA length = 93 bp). I am using PCR amplification with two overhanging primers, both containing Illumina adapter sequences (Universal Adapter & ...
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2answers
129 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)?
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1answer
15 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 ...
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1answer
192 views

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

Scientists how to prove DNA is anti-parallel?
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30 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 ...
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What is the strand specificity of a reference genome?

It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. So here's ...
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0answers
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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 ...
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1answer
36 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 ...
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1answer
36 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 ...
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2answers
35 views

Pyura DNA extraction

I'm am struggling with genomic DNA extraction from different samples of Pyura chilensis; the DNA is degraded as can be seen on the gel. We've always used GeneJET Genomic DNA purification Kit (by ...
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1answer
57 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 ...
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3answers
56 views

Is there any way to tell if a gene is functional for an individual with only a reference sequence and the individual's sequence of the gene?

I have gene sequence of a ton of individuals within a subspecies from cdna and the ncbi IDed sequence as well. Is there any way to tell using just the sequence that the gene for an individual is non-...
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2answers
94 views

Dealing with Repetitive Bases in DNA?

I have been given a project involving a plasmid that contains long stretches of Adenine (60 or 120 bases each). These PolyA stretches are interrupted by the occasional G or C. I understand that ...
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3answers
6k views

How can I preserve hair or saliva for future genome sequencing?

Suppose I want to preserve myself so that I can be reproduced as best as possible, in future or be simulated in future. At the moment full human genome sequencing is a bit expensive. One could get ...
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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 ...
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1answer
55 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 ...
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5answers
531 views

PCR products with no band in gel

I am a PhD student and stuck with the no band in the gel results. I am using the following 1 microliter Primer R (20mM) 1 microliter Primer f (20mM) 1 microliter dNTP (10mM) 1 microliter DNA ...
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2answers
78 views

How to find the amino acid in the DNA protein

3' A T A G T A C C G C A T G T A C G G G C G A G A C A T T C G A G C A T T C A T 5' This a Template DNA. How to find the number of amino acids amino acids ...
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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 ...