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le (5m0s)

## 5.4. The UPGMA algorithm

We know how to fill an array with the values of the distances between sequences, pairs of sequences which are available in the file. This array of distances will be the input of our algorithm for reconstructing phylogenetic trees. The name of this algorithm israther complicated but the method itself is rather simple,too simple indeed. We will see that. The name standsfor Unweighted Pair Group Method with Arithmetic Mean, wewill understand these terms along the presentationof the algorithm. The algorithm starts withan array of distances. Let's take this very simpleexample, it implies seven species and here we have the values of thedistances between these different sequences associated with a species. As you ...
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le (4m55s)

## 4.1. How to predict gene/protein functions?

Last week we have seen that annotating a genome means first locating the genes on the DNA sequences that is the genes, the region coding for proteins. But this is indeed the first step,the next very important step is to be able to predict thefunctions of the genes. That is more correctly, the function of the protein coded by the genes. How can we predict thisgene or function protein? It is essentially based on thefact that we will retrieve genes or protein for which the sequenceis similar and for which we know the function. So we will seehow we can measure and compute the similarity between DNA or protein ...
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le (4m50s)

## 5.3. Building an array of distances

So using the sequences of homologous gene between several species, our aim is to reconstruct phylogenetic tree of the corresponding species. For this, we have to comparesequences and compute distances between these sequences and we have seen last week how we were able to measure the similarity between sequences and we can use this similarity as a measureof distance between sequences. So we will compare pairs of sequences, measure the similarity and store the value of distance, of similarity into what we could call a matrix or an array. Before going further, let's makemore explicit the use of these two terms, they are not equivalentbut some people mix them. The ...
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le (4m46s)

## 3.5. Making the predictions more reliable

We have got a bacterial gene predictor but the way this predictor works is rather crude and if we want to have more reliable results, we have to inject into this algorithmmore biological knowledge. We will use a notion of RBS, RBS stands for Ribosome Binding Sites. What is it? OK. Let's have a look atthe cell machinery or part of it here. You certainly see here that wedeal with a eukaryotes cell. Why? It's because you have anucleus and you remember that the difference between prokaryoticcell and eukaryotic cell lies n the existence of a nucleus. Within the nucleus you have the DNA. The DNA is transcribed into ...
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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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