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2.1. The sequence as a model of DNA
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Descriptif
Welcome back to our course on genomes and algorithms that is a computer analysis ofgenetic information.Last week we introduced the very basic concept in biology that is cell, DNA, genome, genes,proteins and this week we will concentrate on these last two concepts, that is genes and proteins and we will see how proteins are coded by genes and what is the process of translating genes into proteins. Then we will design some algorithms for this translation. But first let's come back on the idea that the sequence, that is the string of characters returning these four letters of the alphabet A, C, G and T is a model of DNA. Is the sequence a good model of DNA? Well, object, it's organized in chromosomes,plasmids, segments and so on. It is compacted within the cellin the nucleus, in the case of eukaryotic cells or directly in the cytoplasm in the case of bacterial cells orprokaryotic cells. This molecule may also be alteredthrough interaction with all the molecules, for example, mutilationand this may be important for the role of DNA into the cell. So again, is the sequence, asequence of characters, which is our computer science subject,is the sequence of characters a good model of DNA whichis a biophysical object? What is a good model? An exact and complete model, certainly not, no model is an exact representation of its object.
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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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2.10. How to find genes?
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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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2.6. Algorithms + data structures = programs
RechenmannFrançoisBy 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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2.9. Whole genome sequencing
RechenmannFrançoisSequencing 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,
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2.4. A translation algorithm
RechenmannFrançoisWe have seen that the genetic codeis a correspondence between the DNA or RNA sequences and aminoacid sequences that is proteins. Our aim here is to design atranslation algorithm, we make the
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1.6. GC and AT contents of DNA sequence
RechenmannFrançoisWe 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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2.6. Algorithms + data structures = programs
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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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1.1. The cell, atom of the living world
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1.9. Predicting the origin of DNA replication?
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2.3. The genetic code
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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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5.5. Differences are not always what they look like
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