Ressource pédagogique : 1.8. Compressing the DNA walk

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We have written the algorithm for the circle DNA walk. Just a precision here: the kind of drawing we get has nothing to do with the physical drawing of the DNA molecule. It is a symbolic representation. It is a way of representing the information content of the sequence as a drawing. Remember that the problem of the algorithm we designed is that it supposes the capacity of drawing several millions or billions of segments on the screen. This is not feasible. No screen will be large enough for that. So, how can we deal with this hardware constraint? Compression is the answer. Let's see that in more details. Remember, for each position here,we draw a segment according to the direction we defined at thebeginning of the first session. And so we get something like that. The idea here is, instead of drawing all these small segments, we will draw a segment like that. For example, every 10 small segments and so on. So of course we reduce the numberof segments which are necessary to draw the DNA walk fora complete sequence. How can we do that? We will define a window. The window is, at any time,a part of the sequence. It has a certain length and withinthis window, we will compute the number of A, C, G and T. And we know how to do that because we have done this kind of operation, in the previous session.

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• biologie application informatique (570.285)

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