2.6. Algorithms + data structures = programs
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,
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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 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
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
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.
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,
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
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
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
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
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 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
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