課程信息
4.7
71 個評分
16 個審閱
Once we have sequenced genomes in the previous course, we would like to compare them to determine how species have evolved and what makes them different. In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. We will encounter a powerful algorithmic tool called dynamic programming that will help us determine the number of mutations that have separated the two genes/proteins. In the second half of the course, we will "zoom out" to compare entire genomes, where we see large scale mutations called genome rearrangements, seismic events that have heaved around large blocks of DNA over millions of years of evolution. Looking at the human and mouse genomes, we will ask ourselves: just as earthquakes are much more likely to occur along fault lines, are there locations in our genome that are "fragile" and more susceptible to be broken as part of genome rearrangements? We will see how combinatorial algorithms will help us answer this question. Finally, you will learn how to apply popular bioinformatics software tools to solve problems in sequence alignment, including BLAST....
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Course 3 of 7 in the

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Beginner Level

初級

Clock

Approx. 17 hours to complete

建議:3 hours/week...
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English

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您將獲得的技能

BioinformaticsGraph TheoryBioinformatics AlgorithmsPython Programming
Stacks

Course 3 of 7 in the

Globe

100% 在線課程

立即開始,按照自己的計劃學習。
Calendar

可靈活調整截止日期

根據您的日程表重置截止日期。
Beginner Level

初級

Clock

Approx. 17 hours to complete

建議:3 hours/week...
Comment Dots

English

字幕:English...

教學大綱 - 您將從這門課程中學到什麼

Week
1
Clock
完成時間為 5 小時

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 個視頻(共 51 分鐘), 2 個閱讀材料, 3 個測驗
Video7 個視頻
From Sequence Comparison to Biological Insights 10分鐘
The Alignment Game and the Longest Common Subsequence Problem 3分鐘
The Manhattan Tourist Problem 6分鐘
The Change Problem 10分鐘
Dynamic Programming and Backtracking Pointers 6分鐘
From Manhattan to the Alignment Graph 9分鐘
Reading2 個閱讀材料
Course Details10分鐘
Week 1 FAQs (Optional)分鐘
Quiz1 個練習
Week 1 Quiz15分鐘
Week
2
Clock
完成時間為 2 小時

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 個視頻(共 11 分鐘), 1 個閱讀材料, 3 個測驗
Video1 個視頻
Reading1 個閱讀材料
Week 2 FAQs (Optional)分鐘
Quiz1 個練習
Week 2 Quiz15分鐘
Week
3
Clock
完成時間為 4 小時

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 個視頻(共 29 分鐘), 1 個閱讀材料, 3 個測驗
Video3 個視頻
Space-Efficient Sequence Alignment 10分鐘
Multiple Sequence Alignment 13分鐘
Reading1 個閱讀材料
Week 3 FAQs (Optional)分鐘
Quiz1 個練習
Week 3 Quiz15分鐘
Week
4
Clock
完成時間為 4 小時

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 個視頻(共 36 分鐘), 1 個閱讀材料, 3 個測驗
Video5 個視頻
Sorting by Reversals 4分鐘
Breakpoint Theorem 5分鐘
Rearrangements in Tumor Genomes 5分鐘
2-Breaks 7分鐘
Reading1 個閱讀材料
Week 4 FAQs (Optional)分鐘
Quiz1 個練習
Week 4 Quiz15分鐘
4.7

熱門審閱

創建者 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

創建者 HNJun 22nd 2017

I have taken courses I, II and III. They were consistently excellent. I plan to go for the next one.

講師

Pavel Pevzner

Professor
Department of Computer Science and Engineering

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

Nikolay Vyahhi

Visiting Scholar
Department of Computer Science and Engineering

關於 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....

關於 Bioinformatics 專項課程

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

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