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1.3. DNA codes for genetic information
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Remember at the heart of any cell,there is this very long molecule which is called a macromolecule for this reason, which is the DNA molecule. Now we will see that DNA molecules support what is called the "genetic information". So, DNAcodes for genetic information. How? If you consider this doublestrand molecule, DNA molecule, you remember that on each strandof the molecule, there is a succession of nucleotides. You can follow these nucleotides and write their name or moreexactly the initial of their name. And you will get what we call the sequence". Look: C, T, A and so on. The process by which you obtain this sequence of characters of letters from the DNA moleculesis called "sequencing". This is a biochemical object. This is a symbolic object which canbe analysed by computer algorithms. Some points of vocabulary here. What is a genome? The genome is,at the same time, first the DNA molecule itself as thesupport of genetic information. This DNA molecule can be organized into chromosome, plasmid, segment and so on. It means thatmost of the time, it is not in one piece only, but in severalpieces, several chromosomes, plasmids, segments and so on.
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1.5. Counting nucleotides
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1.6. GC and AT contents of DNA sequence
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We have designed our first algorithmfor counting nucleotides. Remember, what we have writtenin pseudo code is first declaration of variables. We have several integer variables that are variables which
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1.9. Predicting the origin of DNA replication?
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1.4. What is an algorithm?
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1.7. DNA walk
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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
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1.10. Overlapping sliding window
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We have made some drawings along a genomic sequence. And we have seen that although the algorithm is quite simple, even if some points of the algorithmare bit trickier than the others, we were able to
Avec les mêmes intervenants et intervenantes
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1.1. The cell, atom of the living world
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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
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1.10. Overlapping sliding window
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We have made some drawings along a genomic sequence. And we have seen that although the algorithm is quite simple, even if some points of the algorithmare bit trickier than the others, we were able to
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2.3. The genetic code
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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.
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3.6. Boyer-Moore algorithm
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4.5. A sequence alignment as a path
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Comparing two sequences and thenmeasuring their similarities is an optimization problem. Why? Because we have seen thatwe have to take into account substitution and deletion. During the alignment, the
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5.5. Differences are not always what they look like
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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
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1.5. Counting nucleotides
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2.4. A translation algorithm
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3.1. All genes end on a stop codon
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3.9. Benchmarking the prediction methods
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5.4. The UPGMA algorithm
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