À propos de ce cours
4.5
35 notes
6 avis

Cours 6 sur 7 dans le

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Niveau débutant

Approx. 18 heures pour terminer

Recommandé : 3 hours/week...

Anglais

Sous-titres : Anglais

Cours 6 sur 7 dans le

100 % en ligne

Commencez dès maintenant et apprenez aux horaires qui vous conviennent.

Dates limites flexibles

Réinitialisez les dates limites selon votre disponibilité.

Niveau débutant

Approx. 18 heures pour terminer

Recommandé : 3 hours/week...

Anglais

Sous-titres : Anglais

Programme du cours : ce que vous apprendrez dans ce cours

Semaine
1
4 heures pour terminer

Week 1: Introduction to Read Mapping

<p>Welcome to our class! We are glad that you decided to join us.</p><p>In this class, we will consider the following two central biological&nbsp;questions (the computational approaches needed to solve them are shown in parentheses):</p><ol><li>How Do We Locate Disease-Causing Mutations? (<em>Combinatorial Pattern Matching</em>)</li><li>Why Have Biologists Still Not Developed an HIV Vaccine?&nbsp;(<em>Hidden Markov Models</em>)</li></ol><p>As in previous courses, each of these two chapters is accompanied by a Bioinformatics Cartoon created by talented artist Randall Christopher and serving as a chapter header in the Specialization's bestselling <a href="http://bioinformaticsalgorithms.com" target="_blank">print companion</a>. You can find the first chapter's cartoon at the bottom of this message. </p><p><img src="https://stepic.org/media/attachments/lessons/292/chapter7_cropped.jpg" title="Image: https://stepic.org/media/attachments/lessons/292/chapter7_cropped.jpg" width="528"></p>...
4 vidéos (Total 33 min), 2 lectures, 3 quiz
4 vidéos
Why Do We Map Reads? 7 min
Using the Trie 10 min
From a Trie to a Suffix Tree 11 min
2 lectures
Course Details10 min
Week 1 FAQs (Optional)
1 exercice pour s'entraîner
How Do We Find Disease-Causing Mutations? (Week 1)15 min
Semaine
2
4 heures pour terminer

Week 2: The Burrows-Wheeler Transform

<p>Welcome to week 2 of the class!</p> <p>This week, we will introduce a paradigm called the Burrows-Wheeler transform; after seeing how it can be used in string compression, we will demonstrate that it is also the foundation of modern read-mapping algorithms.</p>...
3 vidéos (Total 21 min), 1 lecture, 2 quiz
3 vidéos
Inverting Burrows-Wheeler 13 min
Using Burrows-Wheeler for Pattern Matching 2 min
1 lecture
Week 2 FAQs (Optional)
Semaine
3
4 heures pour terminer

Week 3: Speeding Up Burrows-Wheeler Read Mapping

<p>Welcome to week 3 of class!</p> <p>Last week, we saw how the Burrows-Wheeler transform could be applied to multiple pattern matching. This week, we will speed up our algorithm and generalize it to the case that patterns have errors, which models the biological problem of mapping reads with errors to a reference genome.</p>...
4 vidéos (Total 22 min), 1 lecture, 3 quiz
4 vidéos
Setting Up Checkpoints 8 min
Inexact Matching 6 min
Further Applications of Read Mapping 2 min
1 lecture
Week 3 FAQs (Optional)
1 exercice pour s'entraîner
How Do We Find Disease-Causing Mutations? (Weeks 2-3)20 min
Semaine
4
1 heure pour terminer

Week 4: Introduction to Hidden Markov Models

<p>Welcome to week 4 of class!</p> <p>This week, we will start examining the case of aligning sequences with many mutations -- such as related genes from different HIV strains -- and see that our problem formulation for sequence alignment is not adequate for highly diverged sequences.</p> <p>To improve our algorithms, we will introduce a machine-learning paradigm called a hidden Markov model and see how dynamic programming helps us answer questions about these models.</p>...
5 vidéos (Total 42 min), 1 lecture, 1 quiz
5 vidéos
Gambling with Yakuza 12 min
From a Crooked Casino to a Hidden Markov Model 9 min
The Decoding Problem 5 min
The Viterbi Algorithm 7 min
1 lecture
Note on This Week's Content10 min
4.5
6 avisChevron Right

Meilleurs avis

par TKJun 29th 2016

One of the best specialization on Coursera. Highly recommended for anyone who wants to apply his/her programming skills to fascinating real-world problems.

par DCSep 16th 2018

Really enjoyed this course. It was great to get to build on work from previous courses.

Enseignants

Avatar

Pavel Pevzner

Professor
Department of Computer Science and Engineering
Avatar

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

À propos de Université de Californie à San Diego

UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory....

À propos de la Spécialisation Bioinformatique

Join Us in a Top 50 MOOC of All Time! How do we sequence and compare genomes? How do we identify the genetic basis for disease? How do we construct an evolutionary Tree of Life for all species on Earth? When you complete this Specialization, you will learn how to answer many questions in modern biology that have become inseparable from the computational approaches used to solve them. You will also obtain a toolkit of existing software resources built on these computational approaches and that are used by thousands of biologists every day in one of the fastest growing fields in science. Although this Specialization centers on computational topics, you do not need to know how to program in order to complete it. If you are interested in programming, we feature an "Honors Track" (called "hacker track" in previous runs of the course). The Honors Track allows you to implement the bioinformatics algorithms that you will encounter along the way in dozens of automatically graded coding challenges. By completing the Honors Track, you will be a bioinformatics software professional! Learn more about the Bioinformatics Specialization (including why we are wearing these crazy outfits) by watching our introductory video. You can purchase the Specialization's print companion, Bioinformatics Algorithms: An Active Learning Approach, from the textbook website. Our first course, "Finding Hidden Messages in DNA", was named a top-50 MOOC of all time by Class Central!...
Bioinformatique

Foire Aux Questions

  • Une fois que vous êtes inscrit(e) pour un Certificat, vous pouvez accéder à toutes les vidéos de cours, et à tous les quiz et exercices de programmation (le cas échéant). Vous pouvez soumettre des devoirs à examiner par vos pairs et en examiner vous-même uniquement après le début de votre session. Si vous préférez explorer le cours sans l'acheter, vous ne serez peut-être pas en mesure d'accéder à certains devoirs.

  • Lorsque vous vous inscrivez au cours, vous bénéficiez d'un accès à tous les cours de la Spécialisation, et vous obtenez un Certificat lorsque vous avez réussi. Votre Certificat électronique est alors ajouté à votre page Accomplissements. À partir de cette page, vous pouvez imprimer votre Certificat ou l'ajouter à votre profil LinkedIn. Si vous souhaitez seulement lire et visualiser le contenu du cours, vous pouvez accéder gratuitement au cours en tant qu'auditeur libre.

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