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le (7m7s)

3.7. Index and suffix trees

We have seen with the Boyer-Moore algorithm how we can increase the efficiency of spin searching through the pre-processing of the pattern to be searched. Now we will see that an alternative way of improving the performance is to pre-process the text itself,the searchable text itself and we will, for that, study two methods, the construction of indexes of fixed length words and the algorithm which uses prefix trees. An index of fixed lengthword, what does it mean? Imagine you have a text, a searchable text, that is a text in which you want to search a pattern,here is quite a short text, the sequence is 14 correctors. We will ...
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le (6m59s)

4.9. Recursion can be avoided: an iterative version

We have written a recursive function to compute the optimal path that is an optimal alignment between two sequences. Here all the examples I gave were onDNA sequences, four letter alphabet. OK. The writing of this recursive function is very elegant but unfortunately we will see now that it isnot very efficient in execution time. Let's see why. Remember the computing schema weapply during the recursion, for example here, to compute the cost of this node, we saw that it was required to computerecursively the cost of that node, that node and that node. OK but to compute the cost of that node here, you need to compute the cost ...
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le (6m58s)

2.7. The algorithm design trade-off

We saw how to increase the efficiencyof our algorithm through the introduction of a data structure. Now let's see if we can do even better. We had a table of index and weexplain how the use of these small arrays allowed us to increase the efficiency that is to reduce the number of comparison to be executed when looking up a triplet in the genetic code. Now what I propose is an alternative to this data structure, it's to compute the indexes. OK. So we have this algorithm which uses here a function. You are now familiar with thisnotion of function, the idea is to fragment the complexity ofan algorithm ...
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le (6m39s)

4.7. Alignment costs

We have seen how we can compute the cost of the path ending on the last node of our grid if we know the cost of the sub-path ending on the three adjacent nodes. It is time now to see more deeply why these costs are used to compute the cost in the last node. So again, we saw how we can compute the cost here of the path ending on that node if we know the cost of the sub-path ending on these three red nodes. Indeed, if we come from that node, the cost on that node will be the cost of that node plus the ...
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le (6m25s)

1.8. Compressing the DNA walk

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 ...
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le (6m23s)

3.4. Predicting all the genes in a sequence

We have written an algorithm whichis able to locate potential genes on a sequence but only on one phase because we are looking triplets after triplets. Now remember that the genes maybe located on different phases and on the two strands. It means that to retrieve all the genes on a genome we have to look on six different sequences, three phases on each strand. Let's looknow how we can deal with this kind of search. First we have to modify a little bit our algorithm so that instead of starting at position One, I want to introduce a variable, a parameter which could be One or Two ...
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Documentaires

le (6m21s)

La passion du dessin et de la préhistoire

Les archéologues découvrent des objets abandonnés par les Hommes préhistoriques dans les sites qu’ils ont habités ou visités. La plupart de ces objets sont ceux du quotidien : des ustensiles, des armes, des outils en pierre, en os, en bois de cervidés ou en ivoire. Certains d’entre eux sont décorés. D’autres traces ont été laissées par ces Hommes ; elles se sont surtout conservées dans les grottes, protégées des assauts du temps. Il s’agit de dessins, gravures ou peintures exécutés sur les parois et les sols. L’art tel qu’il nous est parvenu aujourd’hui n’apparait qu’avec l’Homme moderne (l’Homo sapiens). Les objets décorés ...
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