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list 6 séquences
assignment Niveau : Introductif
chat_bubble_outline Langue : Anglais
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Les infos clés

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timer 24 heures de cours

En résumé

Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different. In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We will encounter a powerful algorithmic tool called dynamic programming that will help us determine the number of mutations that have separated the two genes/proteins. In the second half of the course, we will "zoom out" to compare entire genomes, where we see large scale mutations called genome rearrangements, seismic events that have heaved around large blocks of DNA over millions of years of evolution. Looking at the human and mouse genomes, we will ask ourselves: just as earthquakes are much more likely to occur along fault lines, are there locations in our genome that are "fragile" and more susceptible to be broken as part of genome rearrangements? We will see how combinatorial algorithms will help us answer this question. Finally, you will learn how to apply popular bioinformatics software tools to solve problems in sequence alignment, including BLAST.

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Le programme

  • Week 1 - Week 1: Introduction to Sequence Alignment

    Welcome to class!

    If you joined us in the previous course in this Specialization, then you became an expert at assembling genomes and sequencing antibiotics. The next natural question to ask is how to compare DNA and amino acid sequences. T...

  • Week 2 - Week 2: From Finding a Longest Path to Aligning DNA Strings

    Welcome to Week 2 of the class!

    Last week, we saw how touring around Manhattan and making change in a Roman shop help us find a longest common subsequence of two DNA or protein strings.

    This week, we will study how to find a highest scoring ...

  • Week 3 - Week 3: Advanced Topics in Sequence Alignment

    Welcome to Week 3 of the class!

    Last week, we saw how a variety of different applications of sequence alignment can all be reduced to finding the longest path in a Manhattan-like graph.

    This week, we will conclude the current chapter by cons...

  • Week 4 - Week 4: Genome Rearrangements and Fragility

    Welcome to Week 4 of the class!

    You now know how to compare two DNA (or protein) strings.  But what if we wanted to compare entire genomes? When we "zoom out" to the genome level, we find that substitutions, insertions, and deletions don't tell...

  • Week 5 - Week 5: Applying Genome Rearrangement Analysis to Find Genome Fragility

    Last week, we asked whether there are fragile regions in the human genome. Then, we took a lengthy detour to see how to compute a distance between species genomes, a discussion that we will continue this week.

    It is probably unclear how computing th...

  • Week 6 - Week 6: Bioinformatics Application Challenge
    In the sixth and final week of the course, we will apply sequence alignment algorithms to infer the non-ribosomal code.

Les intervenants

Pavel Pevzner
Department of Computer Science and Engineering

Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering

Nikolay Vyahhi
Visiting Scholar
Department of Computer Science and Engineering


Le concepteur

University of California, San Diego

L' Université de Californie à San Diego est une université publique de recherche sur les concessions de terres à San Diego, en Californie. Établi en 1960 près de la Scripps Institution of Oceanography préexistante, l'UC San Diego est le plus méridional des dix campus de l' Université de Californie et offre plus de 200 programmes menant à un diplôme de premier cycle et des cycles supérieurs, recrutant 33 096 étudiants de premier cycle et 9 872 étudiants des cycles supérieurs. 

L'UC San Diego est considérée comme l'une des meilleures universités au monde. Plusieurs publications ont classé les départements de sciences biologiques et d'informatique de l'UC San Diego parmi les 10 meilleurs au monde.


La plateforme


Coursera est une entreprise numérique proposant des formations en ligne ouverte à tous fondée par les professeurs d'informatique Andrew Ng et Daphne Koller de l'université Stanford, située à Mountain View, Californie.

Ce qui la différencie le plus des autres plateformes MOOC, c'est qu'elle travaille qu'avec les meilleures universités et organisations mondiales et diffuse leurs contenus sur le web.

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