4.3. Measuring sequence similarity

Welcome to this introduction to bioinformatics. We will speak of genomes and algorithms. More specifically, we will see how genetic information can be analysed by algorithms. In these five weeks to

We have seen a nice algorithm to draw, let's say, a DNA sequence. We will see that first, we have to correct a little bit this algorithm. And then we will see how such as imple algorithm can provide

During the last session, I explained several times how it was important to increase the efficiency of sequences processing algorithm because sequences arevery long and there are large volumes of

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

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

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

We have seen that a genomic textcan be indeed a very long sequence of characters. And to interpret this sequence of characters, we will need to use computers. Using computers means writing program.

The notion of gene emerged withthe works of Gregor Mendel. Mendel studied the inheritance on some traits like the shape of pea plant seeds,through generations. He stated the famous laws of inheritance

Getting the sequence of the genome is only the beginning, as I explained, once you have the sequence what you want to do is to locate the gene, to predict the function of the gene and maybe study the

Up to now, to predict our gene,we only rely on the process of searching certain strings or patterns. In order to further improve our gene predictor, the idea is to use, to rely onprobabilistic methods

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