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 ...
  • 6,957
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 ...
  • 67.7k
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 ...
  • 8,759
11 votes
Accepted

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 ...
10 votes
Accepted

What is the difference between second and third generation sequencing

I'm assuming you mean DNA sequencing (excluding things like RNA-seq). Is Sanger sequencing the first generation? From Metzker 2010: The automated Sanger method is considered as a "first-...
  • 4,470
10 votes
Accepted

Why is it harder to sequence plant genomes than animal genomes?

The authors of this 2012 review article summarize the problem well in their introduction: In contrast to the tremendous advances in throughput, assembling sequencing reads remains a substantial ...
10 votes
Accepted

What is the difference between sequence, reads, and contigs of genetic material?

My understanding of those three words as follows: sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences reads ...
  • 166
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 ...
  • 8,108
9 votes
Accepted

In percentage, how much is the human genome (DNA) similar to the mouse genome?

This question cannot be answered as simply as you put it, but it's not too much to elaborate on. The order of the base pairs will be drastically different, but the same proteins and amino acids will ...
  • 134
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 ...
  • 7,779
8 votes

Why is assembling paired end illumina without any input parameters an important problem?

The Next-Gen sequencers cannot sequence a very long stretch of DNA with good reliability (~150 for the recent model- HiSeq2000; even less for older models such as GA (40), GA-II (70), GA-IIx (90)). ...
  • 35.1k
8 votes
Accepted

Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?

In chain-termination sequencing, a population of molecules is detected as opposed to a single one. The readout looks like this: [ http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html ] ...
  • 17.5k
7 votes
Accepted

What is the difference between sequence alignment and sequence assembly?

Sequence alignment It is done for checking sequence similarity between two or more different sequences. This will give information about how two sequences are different, what is their evolutionary ...
  • 2,396
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, ...
  • 22.7k
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 ...
  • 1,562
7 votes
Accepted

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 ...
6 votes
Accepted

Does DNA analysis allow determining amount of chromosomes?

This depends completely on the quality of the DNA. Since each chromosome is essentially a very long strand of DNA, breakages and missing sections are very common in extinct species due to degradation ...
  • 9,364
6 votes
Accepted

Is Sanger sequencing still used in labs, and therefore worth learning?

Sanger sequencing is still used in the labs today - and not only on the side. Next-generation sequencing has its strength when it comes to sequencing very large amounts of DNA (basically whole genomes ...
  • 49.4k
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 ...
  • 67.7k
6 votes
Accepted

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 ...
  • 12.7k
6 votes
Accepted

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 ...
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 ...
  • 1,883
6 votes
Accepted

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 ...
  • 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 ...
6 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 ...
  • 1,731
5 votes

Explanation of the meaning of high-throughput

High-throughput, as indicated by canadianer in their comments refers to amount of data that is processed by the system. Though the answer by CactusWoman would be correct for the case of DNA sequencing,...
  • 35.1k
5 votes
Accepted

Explanation of the meaning of high-throughput

High-throughput sequencing specifically refers to sequencing techniques like Illumina that allow you to sequence massive amounts of DNA at once (hundreds of thousands of strands), as opposed to older ...
  • 2,385
5 votes
Accepted

where to find the relative frequency distribution of synonymous codons

The phenomenon of using different codons with different probabilities is called codon usage bias. How the different codons are used is sometimes pretty different between species and requires some care....
  • 49.4k
5 votes

Is there a known minimal stretch of DNA that can distinguish any two people in the world?

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, ...
  • 1,120
5 votes
Accepted

DNA sequencing problem

Even though you - or the problem did not clarify, I assume in my answer that you work with eukaryote system, even though the principle of the replication is the same. dNTPs do have an OH group on ...
  • 3,078

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