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

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Any noticable differences between data on GenBank and ENA Sequence?

For those of us who have submitted DNA sequence data to public sequence databases: Can you think of any difference in data availability or data retrieval (aside from the idiosyncratic online ...
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1answer
12 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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27 views

sanger sequencing troubleshooting

Dear all. I see not colored peaks in Sanger sequencing results after 300-450 bp. I checked sequencing reaction condition with different templates and specific primers, but didn't solve my problem. I ...
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1answer
72 views

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

Scientists how to prove DNA is anti-parallel?
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23 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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0answers
32 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 ...
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1answer
15 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
17 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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1answer
15 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
38 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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2answers
67 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
22 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 ...
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1answer
26 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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35 views

Sanger sequencing materials

According to the Wikipedia entry on Sanger sequencing, "The classical chain-termination method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, normal ...
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1answer
48 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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0answers
11 views

primer blast for BSP methylation

How can I blast my BSP(Bisulfite sequencing) primers? I designed in this way that C nucleotide converted to T and my primers just sit on the converted DNA! I blast it with Bisearch but I don't know ...
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1answer
14 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 ...
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0answers
32 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 ...
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1answer
44 views

what is CpG coverage? DNA starting material?

referring to this quote from an article about predicting methylation states: "Because of the small amounts of genomic DNA starting material per cell, single-cell methylation analyses are ...
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0answers
72 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
80 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 ...
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0answers
30 views

totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime

I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME. Here is the situation. ...
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2answers
52 views

How to determine which is the nucleotide sequence of a gene?

I have came across a few genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine ...
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2answers
30 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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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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1answer
28 views

DNA Sequencing - Sanger termination method: What effects will more ddNTPs in solution have on the resolution on agarose gel via electrophoresis?

Say instead of a small amount of ddNTPs, you add a significant percent of ddNTPs to dNTPs. I was thinking this would reduce the resolution for larger fragments due to more ddNTPs terminating ...
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1answer
17 views

In a Sanger sequencing, what would be happen if different DNA sequence binds to same primer? And how this situation avoided if problematic?

Sanger's PCR chain-termination sequencing, by its theory, is a simple method to sequence DNA from organisms. But what will happen if there are 2 allelic DNA with same primer binding site, but ...
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Y.pestis Clostridium tertium GC content

I am plotting GC content and Genomic Shifting (ori C, terminus ) about y.pestis and c.tertium. I would like to know Why y. pestis have much more local min and local max other has one local min and one ...
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2answers
106 views

What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
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1answer
35 views

Question regarding stop codon

I just wanted to ask that in a given RNA, If there is a start codon and no stop codon, is it still considered mRNA, I mean can it be translated to a protein ?
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2answers
50 views

Why can't we directly use the DNA instead of the RNA in a DNA microarray analysis? [closed]

When proceeding to a DNA microarray analysis, I saw that the molecule that's taken from the cell is the RNA, which is afterwards converted to DNA by a reverse polymerase. But why not taking directly ...
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1answer
66 views

Cutting of DNA strand [closed]

Would EcoRI cut the following sequence?? 😕 5'CTCGAGTTCGAG3' 3'GAGCTCAAGCTC5' What is the logic of cutting? Please explain how restriction enzymes work.
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0answers
25 views

Will an illumina NGS library build work on previously denatured DNA?

I am trying to map the interaction of a small molecule with cellular genomic DNA using a Chem-seq approach (similar to ChIP-seq). The small molecule is crosslinked to DNA, and the DNA is enriched and ...
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0answers
15 views

Where can I find the genome of Cornu aspersum?

Where can I find the genome of the Common (Garden) Snail Cornu aspersum? I have searched for the genome of Cornu aspersum on Ensembl but I did not find it there. Has this species been sequenced? How ...
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3answers
55 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
85 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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2answers
76 views

Complete human rDNA sequence

I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find ...
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143 views

Is DNase treatment necessary before RNA sequencing?

Is it necessary to treat total RNA with DNase before sequencing it? In particular, if the library prep relies on a poly-A enrichment, is it necessary to remove DNA, knowing that genomic DNA does not ...
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Dominant/recessive T-dna insertions?

In cases with T-DNA insertions in plants - why dont we talk about recessive or dominant traits? Depending on what you insert it should still have these qualities, right?
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1answer
53 views

Is my Y-chromosome the same at 78 as it was at 18?

How accurate is a Y-dna test at age 78?
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18 views

How would transposable elements and recombination affect phylogenetic trees?

I'm hypothesizing connections between concepts learned in my Biology class and I'm trying to see if transposable elements or sexual recombination during prophase I affects how related organisms are to ...
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2answers
34 views

Question about phylogenies and DNA sequencing

I'm reading this web page which talks about phylogenies and DNA sequencing: https://bioinf.comav.upv.es/courses/biotech3/theory/phylogeny.html A certain sentence says, "If we consider dolphins and ...
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190 views

What mutations in the DNA replication machinery would decrease the length of Okazaki fragments?

I just started learning about DNA replication and came across an interesting thought. I know that Okazaki fragments are about 100-200 nucleotides long for eukaryotes, yet if a cell was mutated, is ...
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1answer
37 views

How do you sequence a tree genome? [closed]

I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a ...
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0answers
35 views

DNA Longevity in Keratin, Ivory and other Bioplastics

For how long is DNA viable for extraction and/or sequencing in bioplastics created by the human body? I checked out a few links online, and this article gives a record of about 7000 years for frozen ...
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2answers
57 views

Can PCR duplicates have complementary sequences?

It is common when analyzing paired-end whole-genome shotgun sequencing data to check for and eliminate PCR duplicates. The reasoning is that the probability of sampling a fragment of the genome of the ...
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1answer
543 views

How is DNA testing used to differentiate between different species?

How is DNA testing used to determine that specimens belong to different species, rather than being subspecies, or members of the same species? Usually the definition of species is about the ability to ...
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1answer
237 views

Limitations of Gibson Assembly method

Why is the Gibson assembly method limited to ~8 fragments and what can be done to raise this limit? Why is the method called "seamless" and what are the advantages compared to annealing ...
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2answers
111 views

Repeating sequences of genomes

How can we estimate what portion of a genome is repeating sequences without sequencing it? Thank you
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5answers
379 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 ...