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le (4m46s)

5.2. The tree, an abstract object

When we speak of trees, of species,of phylogenetic trees, of course, it's a metaphoric view of a real tree. Our trees are abstract objects. Here is a tree and the different components of this tree. Here is what we call an edge or a branch. We have nodes, a particular nodeis the root and other nodes are the leaves here terminal nodesand we see that when we draw a tree as an abstract object, we put the root upside and the leaves downside so it's the reverse of a classical natural tree. We need an expression to describe a tree and we will use this kind of expression, how ...
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le (4m30s)

4.2. Why gene/protein sequences may be similar?

Before measuring the similaritybetween the sequences, it's interesting to answer the question: why gene or protein sequences may be similar? It is indeed veryinteresting because the answer is related to the theory ofevolution which is due, as you all know, to Darwin. What Darwinsays is that species evolve in time and there is a creation ofnew species for existing ones. So there is an evolutionof species over time. He was a very thinking man, huh. This evolution can be also seenon the genomic sequences. Let's see this very small and partialtree of life and hypothetical tree of life. Here you have thespecies and you have this phenomenon of speciation giving ...
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le (4m29s)

1.6. GC and AT contents of DNA sequence

We have designed our first algorithmfor counting nucleotides. Remember, what we have writtenin pseudo code is first declaration of variables. We have several integer variables that are variables which cantake as a value an integer. One, two, three minus five and so on. We have the sequence of characters we want to interpret, declare as a character string oflengths and define. Then we have the initializationof our different variables. This symbol is a symbol for assignment, it means that zero becomes the value of total nb, nbT and soon and so on and here we say: index takes the value one. It means that we position at the beginning of ...
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le (4m23s)

4.4. Aligning sequences is an optimization problem

We have seen a nice and a quitesimple solution for measuring the similarity between two sequences. It relied on the so-called hammingdistance that is counting the number of differencesbetween two sequences. But the real situation is a bitmore complex as we'll see now, it needs an adequatesolution and algorithm. Why is it a bit more complex? Let's have a look at thispair of two sequences. If we apply the hamming distance,compute the hamming between these two sequences,we find ten differences. OK. But you must remember thatmutation may be substitution, deletion and insertion. So if wetake into account the deletion and insertion, the situation isvery different in the case of these two sequences. ...
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Entretiens

le (4m23s)

#180 - Thierry Amougou - Economie politique historique du développement réel : Comment penser une émergence économique libératrice du développement réel en Afrique subsaharienne à l’âge de la mondialisation économique ?

... Biographie De formation scientifique (mathématique et sciences naturelles) Thierry Amougou est aujourd’hui considéré comme un économiste hétérodoxe du développement. Il est chercheur associé au CETRI (Centre TRICONTINENTAL) et professeur invité à...
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le (4m12s)

4.6. A path is optimal if all its sub-paths are optimal

A sequence alignment between two sequences is a path in a grid. So that, an optimal sequence alignmentis an optimal path in the same grid. We'll see now that a property of this optimal path provides us with scanned lines for designing an optimization algorithm. The property is the following. A path which is optimal is made up of optimal sub-paths. To prove that, we can start byproving that if a path of length L is optimal then the path of length L minus one is also optimal. This can be proved quiteeasily ad arburdum. That is, you take the hypothesis that the path of length L is optimal ...
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