University of California San Diego
Finding Mutations in DNA and Proteins (Bioinformatics VI)
University of California San Diego

Finding Mutations in DNA and Proteins (Bioinformatics VI)

This course is part of Bioinformatics Specialization

Taught in English

Some content may not be translated

Pavel  Pevzner
Phillip Compeau

Instructors: Pavel Pevzner

15,622 already enrolled

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Course

Gain insight into a topic and learn the fundamentals

4.7

(59 reviews)

Intermediate level
Some related experience required
23 hours (approximately)
Flexible schedule
Learn at your own pace

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Assessments

3 quizzes

Course

Gain insight into a topic and learn the fundamentals

4.7

(59 reviews)

Intermediate level
Some related experience required
23 hours (approximately)
Flexible schedule
Learn at your own pace

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This course is part of the Bioinformatics Specialization
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There are 6 modules in this course

<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>

What's included

4 videos2 readings1 quiz2 app items

<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>

What's included

3 videos1 reading2 app items

<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>

What's included

4 videos1 reading1 quiz2 app items

<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>

What's included

5 videos2 app items

<p>Welcome to week 5 of class!</p> <p>Last week, we introduced hidden Markov models. This week, we will see how hidden Markov models can be applied to sequence alignment with a profile HMM. We will then consider some advanced topics in this area, which are related to advanced methods that we considered in a previous course for clustering.</p>

What's included

5 videos1 reading1 quiz2 app items

<p>Welcome to the sixth and final week of class!</p> <p>This week brings our Application Challenge, in which we apply the HMM sequence alignment algorithms that we have developed.</p>

What's included

1 peer review

Instructors

Pavel  Pevzner
University of California San Diego
16 Courses805,647 learners
Phillip Compeau
University of California San Diego
8 Courses273,813 learners

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4.7

59 reviews

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5

Reviewed on Jul 31, 2021

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Reviewed on Sep 15, 2018

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Reviewed on Jun 22, 2020

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