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23 votes

Is TTGATATAT a gene?

This is a very lazy (biologically) "programmer's definition" of a gene. It would be like if you found a biology textbook that said "a program in C is everything between main( and )"...
Bryan Krause's user avatar
  • 46.2k
16 votes
Accepted

Would it be possible to sequence human DNA from wastewater treatment plants?

As it turns out, you are not the first to have this idea. Prior research claims that it is, at least in principle, possible to conduct epidemiology of cancer by sequencing on wastewater DNA for ...
jakebeal's user avatar
  • 7,007
14 votes

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

Horizontal gene transfer Don't expect to have a tree! Horizontal gene transfer happens and therefore we would end up with a network, not a tree. Gene trees Different DNA sequences have different ...
Remi.b's user avatar
  • 68.3k
12 votes

Could someone explain the join in the SARS-cov-2 genome at location 13468?

In the reference genome browser, it seems you are looking at the first Coding Sequence (CDS) line, YP_009724389.1, which shows the translation to LNRV...: If you look lower down, you'll see a line ...
mgkrebbs's user avatar
  • 9,083
12 votes
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Why are DNA samples stored as biochemical samples and not as binary data?

One reason DNA samples are kept is because we might want to do further analysis using them. If we relied on digital records we'd have to synthesize the physical DNA from the digital record, adding an ...
Charles E. Grant's user avatar
10 votes
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Tips for longer fragment size and higher purity of insect DNA

Insect samples are difficult to work with primarily because they contain a bunch of polysaccharides, like chitins, that are similar enough to nucleic acids that they can co-precipitate. Standard ...
bob1's user avatar
  • 12.5k
9 votes
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Limitations of 16S rRNA sequencing

There is simply no variation in the 16S rRNA gene between different species/strains that it would be useful to tell apart for a more accurate analysis. The amount of sequence variation depends on the ...
acvill's user avatar
  • 8,326
9 votes

Is TTGATATAT a gene?

This isn't the definition of a gene. In many organisms, genes include introns, and the regions upstream and downstream of the starts and stops (untranslated regions, usually called 5' and 3' UTRs), ...
swbarnes2's user avatar
  • 5,230
7 votes
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Are SNPs and alleles the same thing?

Alleles are variations of a same locus that codes for a protein (gene). These alleles can come in different forms, one of which is SNP. For example, sickle cell anemia arises from an allele of the ...
Franco Grosso's user avatar
7 votes
Accepted

What direction is a sequence in databases written?

Directionality It is indeed the convention to represent nucleic acid sequences in the 5ʹ to 3ʹ direction. This is implied in the IUPAC/IUB document on Abbreviations and Symbols for Nucleic Acids, ...
David's user avatar
  • 26.3k
7 votes

Where can I find SARS-CoV-2 genome sequences for the UK?

Oxford University's Bugbank project is designed to collect SARS-CoV-2 samples (and other microbial cultures) from UK Biobank participants for sequencing. Once completed this data will be available to ...
brazofuerte's user avatar
  • 1,582
7 votes
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What were the challenges to sequencing the last 8% of the human genome that took 20 years to overcome and how was this done? (T2T Consortium)

The ~8% of the sequence that was missing was, as you say, complicated by high repeat content. Repeats make the problem of computational genome assembly hard at the best of times. Long repeat arrays ...
Maximilian Press's user avatar
7 votes

Why are DNA samples stored as biochemical samples and not as binary data?

The answer by Charles Grant is absolutely correct, especially with respect to our limitations with sequencing DNA of biological origin. I'd like to add that DNA is also a much more stable storage ...
Darlingtonia's user avatar
  • 2,659
6 votes

Does the cell have a mechanism to determine DNA sequence from protein?

"Reverse translation" Translation is the process by which an mRNA is "translated" into a protein. It is impossible to get the exact DNA sequence from the protein sequence because a large number ...
Remi.b's user avatar
  • 68.3k
6 votes
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Whole Genome Sequencing vs Whole Exome Sequencing

WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only ...
terdon's user avatar
  • 12.9k
6 votes

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

Not the kind of complex phenotype that you describe (because nobody knows for example if/how "being abusive" is written in the genome), but yes, some things can be determined. The easiest is through ...
Mowgli's user avatar
  • 1,929
6 votes
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Why are there two abrupt changes in the genome sequencing price curve?

This graph from the Broad's Opinionome blog (ugh) is somewhat more annotated: As noted elsewhere, the precipitous drop in 2007 is almost certainly due to maturing next-gen sequencing (NGS), in ...
Amory's user avatar
  • 9,701
6 votes

Tips for longer fragment size and higher purity of insect DNA

I think @bob1's answer is good, and covers a lot of the bases. One thing that I think is missing however is the use of a nuclear preparation as an initial step- my understanding is that this can help ...
Maximilian Press's user avatar
6 votes

What does it mean to collapse heterozygous alleles?

I suspect this means that either the multiple alleles are represented with an ambiguity code: Haplotype1: ATCG Haplotype2: ACCG Consensus: AYCG Or,...
Darlingtonia's user avatar
  • 2,659
6 votes
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What is the function of PCR in the whole genome sequencing?

PCR is used to replicate each isolated genome fragment, yielding several copies of each fragment in your DNA solution (that‘s called a library = a collection of fragments + adapters). This amplifies ...
markur's user avatar
  • 1,779
5 votes
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Why is only one primer used for DNA sequencing instead of two?

The reaction for the Sanger sequencing reacting contains beneath the normal dNTP (which are needed to make most of the DNA) the dideoxynucleotides, which lack the 3'-OH-Group and which are labelled ...
Chris's user avatar
  • 51.7k
5 votes
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How is DNA testing used to differentiate between different species?

Statistics of divergence You can compute various statistics of group divergence. Typically you could consider the pairwise number of differences between any pair of individuals. For example the ...
Remi.b's user avatar
  • 68.3k
5 votes

A cure for radiation exposure?

Would that be a good thing? Recent research from the Samson lab at MIT suggests that there are side effects from amplifying the DNA repair mechanism. Hyperactivity of a base-excision repair (BER) ...
Alex Reynolds's user avatar
5 votes
Accepted

Understanding the strategy of Sanger DNA sequencing

If you mark the full length strand of the DNA with the fluorescent labels, you will get a lot of signals from the same nucleotide without the possibility to discriminate where the actual nucleotide is ...
Chris's user avatar
  • 51.7k
5 votes
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How long does foreign DNA stay intact in human blood?

The De Vlaminck Lab has extensively studied the origins of circulating cell-free DNA (cfDNA) in human plasma and its utility in detecting infections and organ injury.1,2 Concerning your question of ...
acvill's user avatar
  • 8,326
5 votes

Population Genetics Using WGS: How do I know when I have enough individuals?

I think that many of the applications that you mention require wildly different numbers of individuals. It would help to know more about goals, questions, organism details, etc. For example, for ...
Maximilian Press's user avatar
5 votes

Would it be possible to sequence human DNA from wastewater treatment plants?

As already hinted in the answer by @jakebeal, the low concentration (high dilution) of human DNA in waste water would mean that we need huge sequencing depth in order to detect something. This is not ...
Roger V.'s user avatar
  • 3,862
5 votes

Limitations of 16S rRNA sequencing

In my experience, the primary impetus is number 3 on your list, but it's also related to number 1. There's a lot you can learn from 16s sequencing, but reviewers want functional data that can help ...
MikeyC's user avatar
  • 4,787
5 votes
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What is the difference between 4th generation sequencing and NGS?

I think that all of this is pure marketing and can be safely ignored. There is no basis for the generations of sequencing in chemistry or instrumentation, except possibly that second-generation (...
Maximilian Press's user avatar
5 votes
Accepted

What results would come from DNA analysis of several different types of DNA mixed together?

You may be interested in commercially available meat testing kits - DNA kits have been widely used to detect what certain food products are actually (or are actually not) made of. Some kits are ...
Nuclear Hoagie's user avatar

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