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le (5m48s)

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, that is, doesit return the expected answer? The answer is yes, if you giveas an input a sequence of DNA, you will get as an output asequence of amino acids unless, of course, one of the tripletsis not one of the 64 expected triplets and then you will get, ofcourse, a nonsense protein sequence. Is it efficient? Well, for measuring the efficiency of an algorithm, you can ask the question, how manybasic operations you have to execute. In ...
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le (6m58s)

2.7. The algorithm design trade-off

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 small arrays allowed us to increase the efficiency that is to reduce the number of comparison to be executed when looking up a triplet in the genetic code. Now what I propose is an alternative to this data structure, it's to compute the indexes. OK. So we have this algorithm which uses here a function. You are now familiar with thisnotion of function, the idea is to fragment the complexity ofan algorithm ...
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le (8m22s)

2.8. DNA sequencing

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 sequences, so it's now the time to ask: but where these sequences come from? This is the process of sequencing. DNA sequencing is a physical operation through which a DNA molecule is read, that is every nucleotide along the strand of the molecule is read and then a text is producedas a succession of the nucleotides as letters. So from the DNA molecule tothe text through what is a sequencer. Sequencers are smaller and smaller and smaller and they ...
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le (5m54s)

2.3. The genetic code

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. There are 20 amino acidsin the living world. They can be named by a single letter,3 letters or their full name. It means that a protein can berepresented by a sequence of letters in a 20 letter alphabet. Let's come back again on thiscorrespondence between gene and protein. Genes are regions of DNA. These regions are first transcribedinto RNA and then RNA into proteins. And proteins’ sequences of aminoacids fold into 3D structures. Like here, some helixes. Translation is the process whichgoes from RNA to ...
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le (4m46s)

3.3. Searching for start and stop codons

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 are codons. You can have triplets outside genes. Within genes, they are called codons. In general, we arelooking for triplets. If you have a sequence like thisone and you are looking for occurrences of this triplet, whatyou have to do is: position your triplet at the beginning of the sequence. Compare the first letter. If it is not ...
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