Об этом курсе
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Курс 6 из 7 в программе

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Начальный уровень

Прибл. 18 часа на выполнение

Английский

Субтитры: Английский

Курс 6 из 7 в программе

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Гибкие сроки

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Начальный уровень

Прибл. 18 часа на выполнение

Английский

Субтитры: Английский

Программа курса: что вы изучите

Неделя
1
4 ч. на завершение

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>

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4 видео ((всего 33 мин.)), 2 материалов для самостоятельного изучения, 3 тестов
4 видео
Why Do We Map Reads? 7мин
Using the Trie 10мин
From a Trie to a Suffix Tree 11мин
2 материала для самостоятельного изучения
Course Details10мин
Week 1 FAQs (Optional)
1 практическое упражнение
How Do We Find Disease-Causing Mutations? (Week 1)15мин
Неделя
2
4 ч. на завершение

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>

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3 видео ((всего 21 мин.)), 1 материал для самостоятельного изучения, 2 тестов
3 видео
Inverting Burrows-Wheeler 13мин
Using Burrows-Wheeler for Pattern Matching 2мин
1 материал для самостоятельного изучения
Week 2 FAQs (Optional)
Неделя
3
4 ч. на завершение

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>

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4 видео ((всего 22 мин.)), 1 материал для самостоятельного изучения, 3 тестов
4 видео
Setting Up Checkpoints 8мин
Inexact Matching 6мин
Further Applications of Read Mapping 2мин
1 материал для самостоятельного изучения
Week 3 FAQs (Optional)
1 практическое упражнение
How Do We Find Disease-Causing Mutations? (Weeks 2-3)20мин
Неделя
4
4 ч. на завершение

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>

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5 видео ((всего 42 мин.)), 2 тестов
5 видео
Gambling with Yakuza 12мин
From a Crooked Casino to a Hidden Markov Model 9мин
The Decoding Problem 5мин
The Viterbi Algorithm 7мин
4.6
Рецензии: 6Chevron Right

Лучшие рецензии

автор: 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.

автор: DCSep 16th 2018

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

Преподаватели

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Pavel Pevzner

Professor
Department of Computer Science and Engineering
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Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

О Калифорнийский университет в Сан-Диего

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....

О специализации ''Биоинформатика'

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!...
Биоинформатика

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