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Mathematicians have always been prone to error. As proofs get longer and more complicated, the question of correctness looms ever larger. Andrew Wiles’ proof of Fermat’s last theorem contained a flaw that was only fixed a year later. Meanwhile, proof assistants — formal tools originally developed in order to verify ...
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 large genomic texts, it is now possible to sequence a whole genome. But it is just thebeginning of the story. The challenge to ...
Based on the principle we statedin the last session, we will now write in pseudo code a firstalgorithm for locating genes on a bacterial genome. Remember first how this algorithm should work, we first need to find two consecutive stop triplets in the same phase, same phase meansthe number of letters between these two ...
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 are looking for triplets. We use the term triplets as long as wehave no proof that they ...
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 different phases and on the two strands. It means that to retrieve all the genes on a genome we have ...
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 will use a notion of RBS, RBS stands for Ribosome Binding Sites. What is it? OK. Let's have ...
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 Binding Site, upstream gene we can make the prediction of the coding sequence more reliable. So it is clear that pattern searching ...
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 improving the performance is to pre-process the text itself,the searchable text itself and we will, for that, study two methods, ...
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. What does it mean? I will firsttake an example, which is not related to genomic but I think it'sgood ...
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 algorithm, are true genes, thatis genes which have a biological existence. Only experimental analysiscan confirm or infirm your predictions. Nevertheless it is interesting and ...
 
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