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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Why aren't there any competing biologies on Earth?

Why aren't there any competing biologies on Earth? I read sci-books about life based on silicon and I've read an article that said that other structures than DNA can encode genetic information. So ...
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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 ...
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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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Are there known genome sequencing issues in E. coli?

Despite the fact that the human genome project was declared "complete" in 2001, there are even now still gaps due to difficult-to-sequence regions of the genome such as telomeres and ...
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1answer
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Are there any animals whose genome haven't been sequenced yet? [closed]

I referred to a few websites and it seems like almost every animal's genome has been sequenced. However, are there any animals that haven't yet been sequenced? If so, can you provide the list here or ...
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1answer
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DNA complementarity against reverse complementarity [duplicate]

I am sorry to bother with this question (i study genetics for about few hours, because I need to understand my data) and I am really confused about these two terms, because I dont know if the books ...
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1answer
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What does genetically tractable strain mean?

I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this ...
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1answer
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Population Genetics Using WGS: How do I know when I have enough individuals?

I am having a difficult time finding information about a minimum threshold for number of individuals to use in wgs pop gen analyses. Are there software or formulas/theory available to determine what ...
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Are archaeological DNA samples (bone fragment) stabilized and isolated the same ways as living saliva samples?

I've been studying how saliva DNA samples are suspended in a stabilization fluid then isolated using magnetic beads. Are old archaeological DNA samples of deteriorating bones put through this same ...
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Predicting how proteins will be cleaved

Is it possible to predict how proteins coded from mRNA will be cleaved? The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you ...
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What are the advantages of long read sequencing for cancer oncogenomic research?

Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
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Poly-G tails in NovaSeq Paired-end sequencing from museum samples

I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years. The DNA I'm analysing has been sequenced by ...
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1answer
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How to identify the subspecies/breed of a bee

I have been a beekeeper for a number of years and originally obtained my first colonies from a guy in my neighbourhood. However, when I sell bees to someone else, they typically ask what species of ...
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1answer
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How long does foreign DNA stay intact in human blood?

How aggressively is foreign DNA in blood targeted and degraded by the human body? I am asking because we have a metagenomics project where we want to detect parasite DNA in the human blood. The ...
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Genome-wide association study (GWAS) search engine?

I am not a biologist and came across the term genome-wide association study or 'GWAS' for the first time today. Now I would like to see if there is a GWAS on the particular condition I am interested ...
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Hybridization capture: Array-capture vs. in solution

If I wanted to utilize hybridization capture for capturing certain genomic regions, I could do it by utilizing complementary probes immobilized on an array or to use the probes in solution and then ...
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1answer
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Looking for study/genome data for HIV in different organs

I am looking for a research study or data base that has HIV genome data available in fasta or similar format. Specifically I need genome data of HIV taken from different organs in the same subject. I ...
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1answer
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Multiple clones Sanger sequencing analysis

I am doing a 96-well arrayed cloning. I have done Gibson, transformations and minipreps in a 96-well format, then sent out the plate for sequencing. Normally, I sequence 3-4 clones and check if the ...
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1answer
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How to identify an unknown species from a .fasta file containing its genome sequences [closed]

I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole. I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) ...
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1answer
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DNA extraction kit for microbial mats, rocks, and soil in a remote area

I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For ...
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1answer
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Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?

I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed ...
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1answer
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?

I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
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1answer
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Which was the first DNA-based genome to be sequenced?

The Wikipedia article on phi X 174 states that: The phi X 174 (or φX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be ...
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2answers
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Polymerase Chain Reaction Specifics

While going over PCR in my biology lecture this week I have come across a few questions I have about this process. First, since PCR focuses on trying to replicate a specific targeted DNA sequence many ...
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Why can DNA tests with mixed DNA of several people not be used to detect a criminal in a database?

Scenario: Two males attack another pair of two males with a weapon. The attackers are fought off and the weapon remains. Why does the police require DNA samples of the two who have been attacked to be ...
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1answer
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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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1answer
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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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1answer
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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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1answer
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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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2answers
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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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1answer
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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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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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1answer
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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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1answer
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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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2answers
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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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2answers
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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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