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2.9. Whole genome sequencing
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Descriptif
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, to sequence the bacillus subtilis bacteria genome took something like ten years,thirty five laboratories and several millions of euros. It was partly a European project,now some hundreds of dollars and it can be done within a day. The human genome project, famoushuman genome project, more than ten years, three billiondollars, 19-91 dollars OK.Tomorrow certainly less than 1000 dollars per genome, it means that we can now sequence humangenomes, not one but many many human genomes for the sake ofcomparison, diagnosis and so on. So this is a good measure in theevolution of the sequencing technologies, a capacity ofsequencing entire genomes, not part of them, not one gene here, onegene there, the whole genome, to have access to the entiregenetic information of a living organism being a virus, bacteria,a human being, a plant and so on. Let's see what the ordersof magnitudes are. A virus like the influenza is ten tothe power of four letters nucleotides. The bacteria, typical bacteria Escherichia coli, E. coli in English: ten tothe power of six letters. Yeast, famous yeast, you certainly appreciate yeast, it's for beer for example: ten tothe power of seven.
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2.6. Algorithms + data structures = programs
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2.1. The sequence as a model of DNA
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2.10. How to find genes?
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2.4. A translation algorithm
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2.7. The algorithm design trade-off
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2.2. Genes: from Mendel to molecular biology
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2.5. Implementing the genetic code
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2.8. DNA sequencing
RechenmannFrançoisDuring 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
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2.3. The genetic code
RechenmannFrançoisGenes 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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1.3. DNA codes for genetic information
RechenmannFrançoisRemember 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
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2.1. The sequence as a model of DNA
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2.10. How to find genes?
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3.8. Probabilistic methods
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4.3. Measuring sequence similarity
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5.3. Building an array of distances
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1.6. GC and AT contents of DNA sequence
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2.5. Implementing the genetic code
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3.3. Searching for start and stop codons
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4.1. How to predict gene/protein functions?
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4.10. How efficient is this algorithm?
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5.7. The application domains in microbiology
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