5.4. The UPGMA algorithm

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

So we understand why gene orprotein sequences may be similar. It's because they evolve togetherwith the species and they evolve in time, there aremodifications in the sequence and that the sequence

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

We will now design a more graphical algorithm which is called "the DNA walk". We shall see what does it mean "DNA walk". Walk on to DNA. Something like that, yes. But first, just have a look again at

By writing the Lookup GeneticCode Function, we completed our translation algorithm. So we may ask the question about the algorithm, does it terminate? Andthe answer is yes, obviously. Is it pertinent,

We have written an algorithm for finding genes. But you remember that we arestill to write the two functions for finding the next stop codonand the next start codon. Let's see how we can do that. We

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

We have seen the principle of an iterative algorithm in two paths for aligning and comparing two sequences of characters, here DNA sequences. And we understoodwhy the iterative version is much more

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