4.4. L’alignement de séquences devient un problème d’optimisation

During the last session, we saw how at the heart of the cell there's DNA in the nucleus, sometimes of cells, or directly in the cytoplasm of the bacteria. The DNA is what we call a macromolecule, that

We have made some drawings along a genomic sequence. And we have seen that although the algorithm is quite simple, even if some points of the algorithmare bit trickier than the others, we were able to

Genes code for proteins. What is the correspondence betweenthe genes, DNA sequences, and the structure of proteins? The correspondence isthe genetic code. Proteins have indeedsequences of amino acids.

We have seen how we can make gene predictions more reliable through searching for all the patterns,all the occurrences of patterns. We have seen, for example, howif we locate the RBS, Ribosome

Comparing two sequences and thenmeasuring their similarities is an optimization problem. Why? Because we have seen thatwe have to take into account substitution and deletion. During the alignment, the

The algorithm we have presented works on an array of distance between sequences. These distances are evaluated on the basis of differences between the sequences. The problem is that behind the

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