5.1. L’arbre des espèces

In this session, don't panic. We will design our first algorithm. This algorithm is forcounting nucleotides. The idea here is that as an input,you have a sequence of nucleotides, of bases, of letters,

We have seen that the genetic codeis a correspondence between the DNA or RNA sequences and aminoacid sequences that is proteins. Our aim here is to design atranslation algorithm, we make the

Last week we studied genes and proteins and so how genes, portions of DNA, are translated into proteins. We also saw the very fast evolutionof the sequencing technology which allows for producing

It is necessary to underline that gene predictors produce predictions. Predictions mean that you have no guarantees that the coding sequences, the coding regions,the genes you get when applying your

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

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

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

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

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

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

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

Remember at the heart of any cell,there is this very long molecule which is called a macromolecule for this reason, which is the DNA molecule. Now we will see that DNA molecules support what is called