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100

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 with perhaps some unidentified genes, pseudogenes, regulatory sequences, etc. Basically, pretty much the entire DNA sequence is available now, not just the gene ...


61

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 human genome for the same 3-tandem repeat CAT sequence results in many hits as well. This is because you are essentially searching for short tandem repeats on ...


43

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 likely have some energetic disadvantage relative to DNA and RNA (e.g., requiring a higher bond formation energy, having a less flexible backbone) and those would ...


16

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 are 3 bases, giving expected number of occurrences in 2.7 Gb as $\frac{2.7 \cdot 10^9}{4^3} \approx 42\,188\,000$ Repeating the calculation for longer ...


16

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 biomarkers. The ethics of this approach also need not be problematic because narrowly targeted sequence amplification focused on biomarkers like SNPs will not ...


14

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 evolutionary histories. See, in particular, the question of incomplete lineage sorting. This means that one may compute a tree for a given DNA sequence that must ...


12

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 for CDS YP_009725295.1, which shows translation to LNGF... as you expected. So, these are two different interpretations of possible translations for this area of ...


11

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 but he won the prize for making specific sequences of RNA bases which were then fed to cells, resulting in specific amino acid chains, which ultimately deciphered ...


10

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 endeavor, much greater than the sequencing efforts alone would suggest [22-24]. Large complex plant genomes remain a particularly difficult challenge for de novo ...


10

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 are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example ...


10

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 was preceded by a prebiotic world where RNA won the competition from rival nucleic acids. Then during the RNA-world period, the RNA-world evolved ever more ...


10

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 extraction procedures (e.g. Qiagen blood/tissue kits) do not handle this well without some modifications to get rid of these contaminants. The slimy aspect of your ...


9

Short Answer In a nutshell, DNA sequencing technology has a limit to how long a stretch of DNA it can read in one go. Long Answer So what most commonly occurs is the length of DNA you wish to sequence needs to be (almost randomly) chopped up into given lengths (depending on the technology) and each length or read is sequenced in parallel. But now you don'...


9

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. You'll need several projectors and a hell of a big wall. (say you take the smallest readable police setting you'll have each letter take a space of 4*6 pixels ...


9

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 be coded for in genes, just at different points along the DNA. For example, you may find the same sequence to code for a protein in a mouse as in a human, but ...


9

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 biologies have zero competitive advantage over each other. The abstract of Emergence of homochirality in large molecular systems (Laurent, Lacoste and Gaspard (...


9

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 region of the 16S rRNA gene amplified, and the choice of region depends on the desired universality of your primers as well as the read length constraints of ...


8

These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, which still contain too much salts from the PCR reactions. This can also happen to only a few bands as seen ...


8

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 sequences belonging to a certain organism or gene. For example, searching for "E coli" will give you the full genome sequences for several bacterial species, ...


8

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)). For increasing the confidence in a certain hit, it was sequenced from both the ends. For example, if you have selected 500bp DNA fragment, then after ligating ...


7

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 recognition site. J Mol. Biol. 51: 393-409 The enzyme was then called endonuclease R, but is now known as HindII (or HincII). The method used was to cut DNA with ...


7

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-generation" technology Some of the technology that was in development when this review was written is no longer in development, but this is still an excellent review ...


7

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 years later... so how did he know? jpa's answer shows that you'd expect to get only about five CATs - not ten, and the chance of getting ten is astronomically ...


7

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, Polynucleotides and their Constituents, although not stated explicitly — presumably because this was written in 1974, before the large nucleic acid databases ...


7

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 researchers through the UK Biobank: We originally developed this system as a pilot study to determine the feasibility of prospective microbiological culture ...


6

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 sterically hindered from digesting protein-bound DNA Immunoprecipitation - this allows isolation of the target protein by binding it to a selective antibody ...


6

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 to repeat the whole thing twice. Second, the technology is such that it's not easy to generate, say, the whole sequence of a chromosome that came from their ...


6

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 over time. If a full DNA read is absent, no determination of chromosomal number can be performed. Assuming a full read (covering all breakages) of the DNA ...


6

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 ] The peaks represent intensity of the four different fluorophores at the detector. Every fragment that is terminated at the same spot will have the same ...


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