99
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 ...
15
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 ...
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 (...
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 v short answer is that in shotgun sequencing, the sequencer is fed a set of random sequences from the target. This can be done for instance by mechanically shearing DNA and then building a set of shotgun sequencing jobs which are then compiled back together by a genome assembler (i.e. in whole genome sequencing projects) into a full sequence.
In ...
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 ...
6
Note that the query sequence you have provided matches the minus strand of your target sequence. That means not only that the target sequence will be reversed (as you have noted), but it will also be complemented as well. So in the GenBank record, you should not look for the sequence CCGACCGA... starting at position 10835, you should look for the sequence ......
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 ...
6
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 or exomes).
Sanger sequencing is used when you want to sequence smaller regions or portions of a genome/plasmid. Typical read length is (depeding on the ...
6
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 makes your analysis harder and doesn't actually add anything useful.
If you know you're interested in CNVs, that's different. CNV detection is hard in general but ...
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