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 )"...
- 44k
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 ...
- 6,977
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 ...
- 68k
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 ...
- 9,024
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 ...
- 3,313
10
votes
Accepted
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 ...
- 11.2k
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
Accepted
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 ...
- 8,266
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), ...
- 5,175
7
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 ...
- 144
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, ...
- 24.3k
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 ...
- 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 ...
- 9,132
6
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
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 ...
- 68k
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 ...
- 12.8k
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 ...
- 1,913
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 ...
- 9,681
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 ...
- 9,132
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 ...
- 2,298
6
votes
Accepted
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 ...
- 1,769
5
votes
Accepted
In DNA sequencing, is "mate pairs" synonymous with "paired ends"? If not, how do they differ?
Paired-end is the name of the sequencing approach.
Mates refer to the read pairs that correspond to the same insert, but sequenced from opposite directions.
- 35.2k
5
votes
How can I generate a random DNA sequence?
If you want to synthesize a specific DNA sequence chemically, you start by attaching your first nucleotide (one letter in your DNA) to a solid phase. You can then continue adding individual letters to ...
- 9,174
5
votes
Accepted
Do plants have distinctive DNA genomes from each other like humans do?
Short answer: Yes!
Now for the longer answer. Yes, they do have distinct genes in general, but what you may see as different plants can also sometimes be clones. For example Quaking Aspen Trees which ...
5
votes
Accepted
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 ...
- 51.5k
5
votes
Accepted
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 ...
- 68k
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) ...
- 5,568
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 ...
- 51.5k
5
votes
Accepted
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 ...
- 8,266
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 ...
- 9,132
Only top scored, non community-wiki answers of a minimum length are eligible