This course is part of the Bioinformatics Specialization

4.7
stars
57 ratings

Pavel Pevzner +1 more instructor

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Bioinformatics SpecializationUniversity of California San Diego

About this Course

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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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Course 6 of 7 in the

Bioinformatics Specialization

Beginner Level

Approx. 23 hours to complete

English

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Flexible deadlines

Reset deadlines in accordance to your schedule.

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Coursera Labs

Includes hands on learning projects.

Learn more about Coursera Labs

Course 6 of 7 in the

Bioinformatics Specialization

Beginner Level

Approx. 23 hours to complete

English

Could your company benefit from training employees on in-demand skills?

Try Coursera for Business

Instructors

Pavel Pevzner

Professor

Department of Computer Science and Engineering

706,641 Learners

14 Courses

Phillip Compeau

Visiting Researcher

Department of Computer Science & Engineering

233,955 Learners

8 Courses

Offered by

University of California San Diego

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Syllabus - What you will learn from this course

Week1

Week 1

4 hours to complete

Week 1: Introduction to Read Mapping

Welcome to our class! We are glad that you decided to join us.In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):<ol><li>How Do We Locate Disease-Causing Mutations? (Combinatorial Pattern Matching)</li><li>Why Have Biologists Still Not Developed an HIV Vaccine? (Hidden Markov Models)</li></ol>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. <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">

4 hours to complete

4 videos (Total 33 min), 2 readings, 3 quizzes

Week2

Week 2

4 hours to complete

Week 2: The Burrows-Wheeler Transform

4 hours to complete

3 videos (Total 21 min), 1 reading, 2 quizzes

Week3

Week 3

4 hours to complete

Week 3: Speeding Up Burrows-Wheeler Read Mapping

4 hours to complete

4 videos (Total 22 min), 1 reading, 3 quizzes

Week4

Week 4

4 hours to complete

Week 4: Introduction to Hidden Markov Models

Welcome to week 4 of class!

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. 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.

4 hours to complete

5 videos (Total 42 min)

Reviews

4.7

13 reviews

5 stars
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4 stars
22.80%
3 stars
1.75%
2 stars
1.75%

TOP REVIEWS FROM FINDING MUTATIONS IN DNA AND PROTEINS (BIOINFORMATICS VI)

by ZXJul 20, 2019

In depth and comprehensive coverage of the topics in genetic data analysis.

by RGApr 13, 2020

It was probably my favorite in this specialization (at least, out of first six).

by SCSep 15, 2018

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

by JMJun 22, 2020

Really loved learning about suffix trees/arrays, BWT, Pattern matching, HMMs!

View all reviews

About the Bioinformatics Specialization

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!

Frequently Asked Questions

When will I have access to the lectures and assignments?
Access to lectures and assignments depends on your type of enrollment. If you take a course in audit mode, you will be able to see most course materials for free. To access graded assignments and to earn a Certificate, you will need to purchase the Certificate experience, during or after your audit. If you don't see the audit option:
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The course may offer 'Full Course, No Certificate' instead. This option lets you see all course materials, submit required assessments, and get a final grade. This also means that you will not be able to purchase a Certificate experience.
What will I get if I subscribe to this Specialization?
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.
Is financial aid available?
Yes. In select learning programs, you can apply for financial aid or a scholarship if you can’t afford the enrollment fee. If fin aid or scholarship is available for your learning program selection, you’ll find a link to apply on the description page.

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Finding Mutations in DNA and Proteins (Bioinformatics VI)

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