4.5. Un alignement de séquences vu comme un chemin dans une grille

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

Welcome back to our course on genomes and algorithms that is a computer analysis ofgenetic information. Last week we introduced the very basic concept in biology that is cell, DNA, genome, genes

Sequencing is anexponential technology. The progresses in this technologyallow now to a sequence whole genome, complete genome. What does it mean? Well let'stake two examples: some twenty years ago,

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

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

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.

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