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Computer programmers, working with molecular geneticists, have developed computer programs that can identify genes within long stretches of DNA sequences. Imagine t...

Question

Computer programmers, working with molecular geneticists, have developed computer programs that can identify genes within long stretches of DNA sequences. Imagine that you are working with a computer programmer on such a project. On the basis of what you know about the process of transcription, what sequences should be used to identify the beginning and end of a gene with the use of this computer program?

Computer programmers, working with molecular geneticists, have developed computer programs that can identify genes within long stretches of DNA sequences. Imagine that you are working with a computer programmer on such a project. On the basis of what you know about the process of transcription, what sequences should be used to identify the beginning and end of a gene with the use of this computer program?



Answers

Bioinformatics includes all of the following except
(A) using computer programs to align DNA
sequences.
(B) using DNA technology to combine DNA from
two different sources in a test tube.
(C) developing computer-based tools for genome analysis
(D) using mathematical tools to make sense of biological
systems.

So we're being asked to the German how we find similarities or region of similarity between cell types or species. Okay. And, um, the question says which sequencing technique is used to accomplish this? And I think the way that this question is worded is slightly confusing because it specifically says sequencing, technique and sequencing technique is a technique that's used to determine the sequence of a poly unit molecule beat a poly peptide or Polly nucleotide or maybe even a poly sec. Arise. Right. So sequencing technique basically is a technique that determines the sequence off the units in the molecule. Sequencing techniques do not compare regions. They did not find regions of similarity between different sequences. They're just they just find sequences. There are other methods to find similarities. OK, so I think, uh, it would make more sense to answer this question if we remove the word sequence and we just say what technique is used to find regions of similarity, that makes a little more sense, right? So if we look at our answer choices uh, the on Lee, uh, the only answer choice that doesn't talk about sequences is Choice B, which talks about sequence alignment. Okay, And that makes sense. Right sequence alignment. You're talking about aligning different sequences, and this is what that looks like. So on the left hand side, we have sequence alignments off different proteins. So this is protein okay, and you have different proteins that are listed this way, and you are aligning their amino acid sequence to basically find how similar all of these different proteins are. And these proteins could be from different cell types or different organisms. Likewise, you can sequence D. N A. Or or in a to basically accomplish the same thing, depending on what's easier at the moment or equipment you have, or depending on the research. Answer that you're tryingto they trying to answer. So basically, you can align sequences of proteins or sequences of DNA and RNA in order to find out similarities between cell types. The the more similar the protein or the D N A. Between two cells or between two organisms, the more closely related they are. So Choice B is the correct answer

All right, We're being asked to determine, um, which of the fooling choices is correct regarding, uh, d n a sequencing methods and their correct description. So let's start with the 1st 1 The chain termination method. The change from an F A termination method is a method where you want to, uh, replica. You want to see once a certain target D n A. And you put that target D n a in a flask. Try and draw last here. All right, you put that DNA in a flask along with some nucleotides, right click. I try phosphates, and along with some dye, the oxy nucleotide try phosphates. Okay? And they go all in there with the DNA and as the DNA is growing. So let me go over here now. All right, So this is our target, D n a. And you. You put a primer on the DNA and you start replicating with Vienna after the primer. Now, as the DNA starts growing, um, it's gonna get incorporated regular nuclear ties in there, but sometimes just by chance alone since they are in solution, the diet Dina di di Oxy nucleotide will get incorporated into the chain and that can happen either towards the beginning, towards the end or somewhere in the middle. And the addition off a dye, the oxy nucleotide to the chain terminates replication. It stops replication, right, which is why it's called chain termination Method. So basically, you start producing a bunch of different chains and just by chance alone, those chains are going toe. Stop reproducing or not not read this. We are going to stop being replicated at some point in time just by the addition off the dive, the Oxy nuclear tie. And then you sequence all of those chains and you can then see that. Okay, if the replicated thing if the replicated DNA is one nucleotide long and the first dd NTP that was incorporated is a G than the first letter is a G and then you say OK, if the replicated d n a stretches two nucleotides long and the second letter is a tea, well, then we now that we have g and T for the first right for the first and second. So now that you know the first and second you pick the fragment with three nucleotides law and that one is also a tea. Okay, so we have G TT, and that's how you build the entire sequence. And this is a little bit time consuming, but this is how we first used to um uh, determine the sequence off D N A. Now let's move into shotgun sequencing. So shotgun sequencing basically does multiple, uh, change termination methods at once. So instead of just taking one instead of just taking one fragment of the n A and making a bunch of different length replications of that and then sequencing, it's one of those. What you do instead is you take the D N A. You break it into a bunch of different fragments and then you sequence every single one of those fragments by the corporation of the D N tp here. So you basically determine what that last Ah ah nucleotide was here. And once you have all the different fragments, you can align them by finding sequences of similarity. So you're like, OK, this is an overlap. So that means that the end off this fragment must match to the beginning of that fragment. So you incorporate that into the sequence and at the end you have the sequence off the large in the molecule. It's called shotgun sequences because you basically do a bunch of the same time, not one at a time. And a next gen sequencing. Um, I don't have a good graphic for this, but it is basically an automated process that performs thousands of these guys simultaneously. So it's an automated process with, like a robotic arms. Everybody pipettes and the DNA sequences get, uh, get determined. And then those sequences are a line in the computer, and the computer spits out one long D n a sequence. So that's how that works. Now let's look at our answer choices. Choice. A change termination method is automated sequences are well, that is wrong right away because in change termination, which was this first guy over here? This is how we used to do it. Back in the day, there was no automated sequence. There's here. Choice Be change Termination A Change Termination Method Inc of DD entities during d n. A. Replication. Yes, shotgun sequencing. Cutting DNA into random fragments sequence using transformation and assembling overlapping sequences. Yes, that is correct. Choice. The next Ah thing in choice B is next generation sequencing automated sequences. Sequencers are used to generate sequences of short fragments, and that is correct because it is automated. Choice E is wrong because, well, actually, let me read it to you. And then so choice. A sea change Termination Method Inc off dd ntp during the DNA replication. Yes, that is correct. Shotgun sequencing. Automated sequences are used. No in shotgun sequences, you don't have automated sequence. There's so choice, he's wrong and Choice d that's wrong for the same reason it's choice A because it says that automated sequencers are used in turning the chain termination method. So the only, uh, answer here that has all of the correct descriptions is Choice B.

Secrecy. Humans, you know, now, as toe identified, the insists causing mechanism bunch in that it Mabel, and we are able to prescribe just to treat these conditions and either cure them or slow down disease progression. Such examples include calling my lawyer genius leukemia or so long as C am el. So for CME tell because off saying out is because off camo, so much chest location between the homo zones, so less Jordan. So the best Rome ozone is Formoso number nine. And this a Banco Bozano is for most. So that is a chromosomal translocation between this chromosome and to create another chromosome in Khost. Um, cost the dude if it be tiles and Chi Mei's. So this is Billy. And we know that this big titles economies were able to block it until in debate is a soul designed this design, a drug court met. He is able to block the 80 findings that a debate the kindness that big thing people by sequencing the human

For the A C. Quincy, um, is done by you, Weiqing A long strip off doing a multi, but heinie. But money and you case it was each month he was in Sandra Sequencing did her me the nuclear that sequences off this equipment. And then after that, we can combine them together. And compared with me reference see, grows. Yeah, A But we'll find out revelations in simple In this, um, this bird Asian can new inches and self. The new patients at Kate and solve the limitations are not leaving. So the help kept prohibition us. I know that this mutation and advice whether new June is OK or the idea that big, huge call it on. This is us such s cancer. On the other hand, for my core away it is again on. So for my core rate, because we are my costa coffee sliced the window with thousands off tiny spots in the divine position. So let's say basis, Michael, always like in that tiny spots, the only on board each spot there is a spacey paper attached tweet and only the specific being a or I'm a is ableto fight with these pro and they each Michael arrayed. She can cover up to buy 100,000 who therefore this cannot address unstable with thousands off being a or on any other since high and, you know wise you. So let's smoke How walks to bang out jeans. So let's say these things while we call Mozo more region and we have folks toe these chromosome region, I say, is over here here, here on We also have a test symbol and the limp wrist and both. So let's say after you had dies Asia. We have four copies off reference and ball. Yeah, A. And we could be referenced. And both being a hoping is using Mollison's and for assemble be used, Lawrence's. Nobody has both being a copy gamble, and that is this region in detests on both Best Buy. We're as better Lucy. More copy number in because sambal Let's see, he has six copies and in the region, that's that. That that that is less copy number in the Nuba symbol. Yes, it didn't have full so I thought he had a decision that able to look at a signal and becoming rather than on present bogus every but the really lose this thing sold, I say. Or the noble. It's a instances issued out, you know? I have, you know, and then would even. But why's your appear as great in border? Believe that while you're appear on screen, therefore, by looking at the Florence, is there anybody who held bed of be on any chromosomal? It was us. Have fun in the present bowl and see if there's, um, cold up border all disease dream.


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