100
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Does the string "...CATCAT..." appear in the DNA of Felis catus?
The Felis catus genome has been published, annotated, and updated quite a bit since 1996, including spans of so-called intergenic regions, which are basically scaffolding and other structures, along ...
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62
votes
Does the string "...CATCAT..." appear in the DNA of Felis catus?
While Matt's answer is perfectly correct, it is important to note that the sequence $(CAT)_n$ in DNA is not restricted to cats, and you would expect to find it anywhere.
For example, searching the ...
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43
votes
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Why aren't there any competing biologies on Earth?
There are indeed almost certainly other potential alternatives to DNA-based biology and the RNA-based biology that may have predated it, which could be used to form viable organisms.
Many of them ...
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16
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Does the string "...CATCAT..." appear in the DNA of Felis catus?
To augment the other answers, let's compute the probability of CATCATCATCAT occurring in random DNA sequence.
Cat DNA length is 2.7 gigabases (source), and there are 4 possible bases.
For 1 CAT there ...
- 301
16
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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 ...
- 6,917
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 ...
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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 ...
- 8,718
11
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How were the first primers made?
The MIT synthetic chemist Gobind Khorana won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids. The chemistry was difficult at the time ...
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10
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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-...
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10
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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 ...
- 515
10
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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
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Why aren't there any competing biologies on Earth?
Jack Szostak's research group has looked at alternatives for RNA as replicators, see e.g. here, and they found that RNA is a far better replicator than the alternatives. So, it seems that RNA-World ...
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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 ...
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9
votes
How can I find a complete human genome file
Non-biologist here stepping in.
@swbarnes2 has a good point pinning the fact that (approx) 3Giga nucleotides to display "on a wall" (as you state) even with a good projector is gonna be a hard task.
...
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9
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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 ...
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9
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Why aren't there any competing biologies on Earth?
While the discussion of heterochirality was squelched I think it deserves to be addressed explicitly, because unlike most "competing biologies" that one might imagine complementary chiral ...
- 4,885
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 ...
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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)). ...
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8
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Looking for a DNA sequence
There are several nucleotide sequence datbases available. One of the largest is the NCBI GenBank at http://www.ncbi.nlm.nih.gov/genbank/
You may use the search bar at the top to search for nucleotide ...
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8
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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 ]
...
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8
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Does the string "...CATCAT..." appear in the DNA of Felis catus?
So, there are a few great answers here already, but it seems nobody addressed an interesting part of your question: GEB was published in 1978 and the genome of Felis catus was not sequenced until many ...
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7
votes
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How was Restriction Site of EcoRI sequenced?
The first determination of a recognition site for a restriction endonulease was reported in:
Kelly & Smith (1970) A restriction enzyme from Hemophilus influenzae II. Base sequence of the ...
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7
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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, ...
- 22.3k
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 ...
- 1,552
7
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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 ...
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6
votes
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introduction to Chip Seq
The basic steps of ChIP-Seq are:
Crosslinking proteins to DNA - this fixes the proteins in their natural positions
Nuclease digestion - this removes regions that are unbound to protein; nucleases are ...
- 17.5k
6
votes
How can I find a complete human genome file
but aren't there 46 chromosomes to include or are some of those
duplicates
First of all, while each person has 2 copies of each chromosome, those copies are 99% identical. So it would be a waste ...
- 4,680
6
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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 ...
- 9,304
6
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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 ...
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