Chromosome Xyz Homework

UPDATE


Before coming to sequencing you have to consider that you are not sequencing a single chromosome from a single cell. You are sequencing a DNA sample corresponding to a population of cells, containing all the chromosomes. I do not know of a procedure to target a single chromosome, targeted procedures for specific regions on the genome sorrounding genes are in existence.

Or is my entire undertanding flawed?

Yes, I would say lacking not flawed.

That said,

So if I say sequencing chromosome1, what does that actually mean?

Hypothetically that would mean you are sequencing DNA from chromosome 1 corresponding to a population of cells. Meaning you are retrieving the sequence of chromosome 1 for usage in downstream analysis by polymerizing its complementary DNA sequence by taking advantage of the procedure of DNA replication.

Which of the two chromosome's gets sequenced?

There is no way to differentiate between two chromosomes in mainstream sequencing experiments. The cell does not have an idea about which chromosome is which and neither do you, so both chromosomes get sequenced at the same time. Please note, I said no way to differentiate between two chromosomes in mainstream sequencing experiments

do comparison take place between two+two=four chromosome1's?

This has two parts. What do you mean by four? If you are implying that chromosome 1 has two strands and that equates to 4 then no, the two strands together make one chromosome. Your cell has 2n or two chromosome 1's. If you are sequencing a population of cells (let's say 1000), you have two thousand chromosome 1's which are being sequenced all of which are present in pairs across 1000 cells.

Do comparisons take place?

In mainstream experiments we do not compare. That said, methods for differentiating between the two chromosome 1's exist. The oldest I could find is an article by M Nagano on allele specific sequencing. In this case, since your parents equally contribute towards your DNA, each of them carry some mutations specific for their DNA. Using this feature we can differentiate between the paternal and maternal chromosome 1.

There's also single cell sequencing, in this case you would be sequencing the two chromosome 1's from a single cell, theoretically you can then also do allele specific sequencing on a single cell allowing you to differentiate between the two chromosome 1's present in the cell.

Finally, there is no way to differentiate the two strands, after sequencing when you align your data back to the reference genome, you will get to know the strandedness of the data.

Answer to old question


Nowadays the word sequencing is synonymous with High-throughput sequencing, and the article you linked to in the comment relates also to high-throughput sequencing techniques (I got this from a cursory glance).

While sequencing dna which of the two strands get sequenced?

Both get sequenced.

In what order is the results provided

Random

while sequencing how are these two strands sequenced?

If it is single end sequencing, we do not know which strand was sequenced first. (There are ways, but for simplicity's sake let's not go there)

If it is paired end sequencing, one read originates from the sense strand and the other read originates from the opposite strand.

You can watch a youtube video here to find out what is the difference

Is it that result of one strand is provide first followed by the other or is it that only one of the two strands get sequenced?

Both are reported.

The question you have asked is very broad, I can go on for a handful of A4 pages and still not finish. Coming to your first question, I said both get sequenced, because we have no way of knowing while sequencing which strand is getting sequenced (there are stranded sequencing techniques, but you should digest what is mentioned/linked here first and later on with some more research come back with a question on stranded sequencing).

After sequencing you get your result in random order, because what you get is not really result but more raw data files which are called FASTQ files. Read up on FASTQ a bit. After sequencing you don't really get a FASTQ but you get a BCL or base call file, which must be converted to FASTQ. These FASTQ must then be either filtered or not based on quality then aligned to a reference genome. This is where you get to know which read came from which strand.

You should read up more on single end sequencing and paired end sequencing to better understand how DNA is sequenced. Also check out this video. This is the most simplified version which I could find. It should make you curious without bombarding you with too much information.

Last of all, in a single end sequencing you have no way of knowing without alignment which strand got sequenced, but in paired end (where a DNA fragment is sequenced from both ends, generating two paired reads) generally, one mate aligns to the sense strand while the other aligns to the antisense strand.

Name: 4 6. (5 points) Suppose that Jane and John are both carriers for galactosemia (a rare autosomal recessive disease.) If they have three children, what is the probability their three children will have three different genotypes? Show your work and Circle your answer. 6*1/4*1/4*1/2 = 3/16 = 0.1875 7. (6 points) Alex, his mother, his father, and his older sister have blood type B. His younger sister and his brothers have type O. Anna, her mother, her father, and her younger brother have type A. Her sister and her older brother have type O. If Alex and Anna have three children, what is the probability at least one of them will have type O? Show your work and circle your answer. (Chance of Alex is I B i) x (Chance of Anna is I A i) x (1-none have type O) = =(2/3) x (2/3) x (1-.75 3 ) = 0.257 = 25.7% 8. (7 points) If three six-sided dice are rolled, what is the probability that the total number of spots showing is 15? Show your work and Circle your answer = P[5, 5, 5] + P[6, 6, 3] P[6, 5, 4] =1/6^3 + 3*1/6^3 + 6*1/6^3 =10/216 = 5/108 =0.0463

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