About this Course
4.7
75 ratings
16 reviews
Specialization

Course 3 of 7 in the

100% online

100% online

Start instantly and learn at your own schedule.
Flexible deadlines

Flexible deadlines

Reset deadlines in accordance to your schedule.
Beginner Level

Beginner Level

Hours to complete

Approx. 17 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English

Skills you will gain

BioinformaticsGraph TheoryBioinformatics AlgorithmsPython Programming
Specialization

Course 3 of 7 in the

100% online

100% online

Start instantly and learn at your own schedule.
Flexible deadlines

Flexible deadlines

Reset deadlines in accordance to your schedule.
Beginner Level

Beginner Level

Hours to complete

Approx. 17 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English

Syllabus - What you will learn from this course

Week
1
Hours to complete
5 hours to complete

Week 1: Introduction to Sequence Alignment

<p>Welcome to class!</p><p>If you joined us in the previous course in this Specialization, then you became an expert at <em>assembling</em> genomes and sequencing antibiotics. The next natural question to ask is how to compare DNA and amino acid sequences. This question will motivate this week's discussion of <strong>sequence alignment</strong>, which is the first of two questions that we will ask in this class (the algorithmic methods used to answer them are shown in parentheses):</p><ol><li>How Do We Compare DNA Sequences? (<em>Dynamic Programming</em>)</li><li>Are There Fragile Regions in the Human Genome? (<em>Combinatorial Algorithms</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. Why have taxis suddenly become free of charge in Manhattan? Where did Pavel get so much spare change? And how should you get dressed in the morning so that you aren't late to your job as a crime-stopping superhero? Answers to these questions, and many more, in this week's installment of the course.</p><p><img src="http://bioinformaticsalgorithms.com/images/cover/alignment_cropped.jpg" width="528"></p>...
Reading
7 videos (Total 51 min), 2 readings, 3 quizzes
Video7 videos
From Sequence Comparison to Biological Insights 10m
The Alignment Game and the Longest Common Subsequence Problem 3m
The Manhattan Tourist Problem 6m
The Change Problem 10m
Dynamic Programming and Backtracking Pointers 6m
From Manhattan to the Alignment Graph 9m
Reading2 readings
Course Details10m
Week 1 FAQs (Optional)
Quiz1 practice exercise
Week 1 Quiz15m
Week
2
Hours to complete
2 hours to complete

Week 2: From Finding a Longest Path to Aligning DNA Strings

<p>Welcome to Week 2 of the class!</p> <p>Last week, we saw how touring around Manhattan and making change in a Roman shop help us find a longest common subsequence of two DNA or protein strings.</p> <p>This week, we will study how to find a highest scoring alignment of two strings. We will see that regardless of the underlying assumptions that we make regarding how the strings should be aligned, we will be able to phrase our alignment problem as an instance of finding the longest path in a directed acyclic graph.</p>...
Reading
1 video (Total 11 min), 1 reading, 3 quizzes
Reading1 reading
Week 2 FAQs (Optional)
Quiz1 practice exercise
Week 2 Quiz15m
Week
3
Hours to complete
4 hours to complete

Week 3: Advanced Topics in Sequence Alignment

<p>Welcome to Week 3 of the class!</p> <p>Last week, we saw how a variety of different applications of sequence alignment can all be reduced to finding the longest path in a Manhattan-like graph.</p> <p>This week, we will conclude the current chapter by considering a few advanced topics in sequence alignment. For example, if we need to align long strings, our current algorithm will consume a huge amount of memory. Can we find a more memory-efficient approach? And what should we do when we move from aligning just two strings at a time to aligning many strings?</p>...
Reading
3 videos (Total 29 min), 1 reading, 3 quizzes
Video3 videos
Space-Efficient Sequence Alignment 10m
Multiple Sequence Alignment 13m
Reading1 reading
Week 3 FAQs (Optional)
Quiz1 practice exercise
Week 3 Quiz15m
Week
4
Hours to complete
4 hours to complete

Week 4: Genome Rearrangements and Fragility

<p>Welcome to Week 4 of the class!</p> <p>You now know how to compare two DNA (or protein) strings. &nbsp;But what if we wanted to compare entire genomes? When we "zoom out" to the genome level, we find that substitutions, insertions, and deletions don't tell the whole story of evolution: we need to model more dramatic evolutionary events known as <strong>genome rearrangements</strong>, which wrench apart chromosomes and put them back together in a new order. A natural question to ask is whether there are "fragile regions" hidden in your genome where chromosome breakage has occurred more often over millions of years. This week, we will begin addressing this question by asking how we can compute the number of rearrangements on the evolutionary path connecting two species.</p> <p>You can find this week's Bioinformatics Cartoon from Randall Christopher at the bottom of this E-mail. What do earthquakes and a stack of pancakes have to do with species evolution? Keep learning to find out!</p> <p><img width="528" src="http://bioinformaticsalgorithms.com/images/cover/rearrangements_cropped.jpg"></p>...
Reading
5 videos (Total 36 min), 1 reading, 3 quizzes
Video5 videos
Sorting by Reversals 4m
Breakpoint Theorem 5m
Rearrangements in Tumor Genomes 5m
2-Breaks 7m
Reading1 reading
Week 4 FAQs (Optional)
Quiz1 practice exercise
Week 4 Quiz15m
4.7
16 ReviewsChevron Right

Top Reviews

By AHAug 19th 2016

A very well taught course that gives you the ins and outs of sequence comparision and introduces chromosme rearrangement analysis in a succint manner. This was

By PBNov 30th 2017

This course was harder than the previous one, I am happy to have made it to the end!

Instructors

Avatar

Pavel Pevzner

Professor
Department of Computer Science and Engineering
Avatar

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering
Avatar

Nikolay Vyahhi

Visiting Scholar
Department of Computer Science and Engineering

About 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....

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!...
Bioinformatics

Frequently Asked Questions

  • 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.

More questions? Visit the Learner Help Center.