Acerca de este Curso
4.5
29 calificaciones
5 revisiones
In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins. In the first half of the course, we would like to ask how an individual's genome differs from the "reference genome" of the species. Our goal is to take small fragments of DNA from the individual and "map" them to the reference genome. We will see that the combinatorial pattern matching algorithms solving this problem are elegant and extremely efficient, requiring a surprisingly small amount of runtime and memory. In the second half of the course, we will learn how to identify the function of a protein even if it has been bombarded by so many mutations compared to similar proteins with known functions that it has become barely recognizable. This is the case, for example, in HIV studies, since the virus often mutates so quickly that researchers can struggle to study it. The approach we will use is based on a powerful machine learning tool called a hidden Markov model. Finally, you will learn how to apply popular bioinformatics software tools applying hidden Markov models to compare a protein against a related family of proteins....
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Beginner Level

Nivel principiante

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Approx. 18 hours to complete

Sugerido: 3 hours/week...
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English

Subtítulos: English...
Globe

Cursos 100 % en línea

Comienza de inmediato y aprende a tu propio ritmo.
Calendar

Fechas límite flexibles

Restablece las fechas límite en función de tus horarios.
Beginner Level

Nivel principiante

Clock

Approx. 18 hours to complete

Sugerido: 3 hours/week...
Comment Dots

English

Subtítulos: English...

Programa - Qué aprenderás en este curso

Week
1
Clock
4 horas para completar

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>...
Reading
4 videos (Total: 33 min), 2 readings, 3 quizzes
Video4 videos
Why Do We Map Reads? 7m
Using the Trie 10m
From a Trie to a Suffix Tree 11m
Reading2 lecturas
Course Details10m
Week 1 FAQs (Optional)m
Quiz1 ejercicio de práctica
How Do We Find Disease-Causing Mutations? (Week 1)15m
Week
2
Clock
4 horas para completar

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>...
Reading
3 videos (Total: 21 min), 1 reading, 2 quizzes
Video3 videos
Inverting Burrows-Wheeler 13m
Using Burrows-Wheeler for Pattern Matching 2m
Reading1 lectura
Week 2 FAQs (Optional)m
Week
3
Clock
4 horas para completar

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>...
Reading
4 videos (Total: 22 min), 1 reading, 3 quizzes
Video4 videos
Setting Up Checkpoints 8m
Inexact Matching 6m
Further Applications of Read Mapping 2m
Reading1 lectura
Week 3 FAQs (Optional)m
Quiz1 ejercicio de práctica
How Do We Find Disease-Causing Mutations? (Weeks 2-3)20m
Week
4
Clock
1 hora para completar

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>...
Reading
5 videos (Total: 42 min), 1 reading, 1 quiz
Video5 videos
Gambling with Yakuza 12m
From a Crooked Casino to a Hidden Markov Model 9m
The Decoding Problem 5m
The Viterbi Algorithm 7m
Reading1 lectura
Note on This Week's Content10m
4.5

Principales revisiones

por 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.

por DCSep 16th 2018

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

Instructores

Pavel Pevzner

Professor
Department of Computer Science and Engineering

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

Acerca de University of California 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....

Acerca del programa especializado Bioinformatics

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!...
Bioinformatics

Preguntas Frecuentes

  • Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.

  • When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.

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