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 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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 = ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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?
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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 ...
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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, ...
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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 ...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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