We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets.
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基因组数据科学 专项课程约翰霍普金斯大学课程信息
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学生职业成果
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完成这些课程后已开始新的职业生涯
33%
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第 4 门课程（共 8 门）
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完成时间大约为12 小时
英语（English）
字幕：阿拉伯语（Arabic）, 法语（French）, （欧洲人讲的）葡萄牙语, 中文（简体）, 意大利语, 越南语, 韩语, 德语（German）, 俄语（Russian）, 土耳其语（Turkish）, 英语（English）, 西班牙语（Spanish）
您将获得的技能
Bioinformatics AlgorithmsAlgorithmsPython ProgrammingAlgorithms On Strings
学生职业成果
43%
完成这些课程后已开始新的职业生涯
33%
通过此课程获得实实在在的工作福利
可分享的证书
完成后获得证书
100% 在线
立即开始，按照自己的计划学习。
第 4 门课程（共 8 门）
可灵活调整截止日期
根据您的日程表重置截止日期。
完成时间大约为12 小时
英语（English）
字幕：阿拉伯语（Arabic）, 法语（French）, （欧洲人讲的）葡萄牙语, 中文（简体）, 意大利语, 越南语, 韩语, 德语（German）, 俄语（Russian）, 土耳其语（Turkish）, 英语（English）, 西班牙语（Spanish）
提供方
约翰霍普金斯大学
The mission of The Johns Hopkins University is to educate its students and cultivate their capacity for life-long learning, to foster independent and original research, and to bring the benefits of discovery to the world.
教学大纲 - 您将从这门课程中学到什么
完成时间为 4 小时
DNA sequencing, strings and matching
This module we begin our exploration of algorithms for analyzing DNA sequencing data. We'll discuss DNA sequencing technology, its past and present, and how it works.
完成时间为 4 小时
19 个视频 （总计 112 分钟）, 7 个阅读材料, 2 个测验
19 个视频
Lecture: Why study this?4分钟
Lecture: DNA sequencing past and present3分钟
Lecture: Genomes as strings, reads as substrings5分钟
Lecture: String definitions and Python examples3分钟
Practical: String basics 7分钟
Practical: Manipulating DNA strings 7分钟
Practical: Downloading and parsing a genome 6分钟
Lecture: How DNA gets copied3分钟
Optional lecture: How second-generation sequencers work 7分钟
Optional lecture: Sequencing errors and base qualities 6分钟
Lecture: Sequencing reads in FASTQ format4分钟
Practical: Working with sequencing reads 11分钟
Practical: Analyzing reads by position 6分钟
Lecture: Sequencers give pieces to genomic puzzles5分钟
Lecture: Read alignment and why it's hard3分钟
Lecture: Naive exact matching10分钟
Practical: Matching artificial reads 6分钟
Practical: Matching real reads 7分钟
7 个阅读材料
Welcome to Algorithms for DNA Sequencing10分钟
Pre Course Survey10分钟
Syllabus10分钟
Setting up Python (and Jupyter)10分钟
Getting slides and notebooks10分钟
Using data files with Python programs10分钟
Programming Homework 1 Instructions (Read First)10分钟
2 个练习
Module 130分钟
Programming Homework 130分钟
完成时间为 3 小时
Preprocessing, indexing and approximate matching
In this module, we learn useful and flexible new algorithms for solving the exact and approximate matching problems. We'll start by learning Boyer-Moore, a fast and very widely used algorithm for exact matching
完成时间为 3 小时
15 个视频 （总计 114 分钟）, 1 个阅读材料, 2 个测验
15 个视频
Lecture: Boyer-Moore basics8分钟
Lecture: Boyer-Moore: putting it all together6分钟
Lecture: Diversion: Repetitive elements5分钟
Practical: Implementing Boyer-Moore 10分钟
Lecture: Preprocessing7分钟
Lecture: Indexing and the k-mer index10分钟
Lecture: Ordered structures for indexing8分钟
Lecture: Hash tables for indexing7分钟
Practical: Implementing a k-mer index 7分钟
Lecture: Variations on k-mer indexes9分钟
Lecture: Genome indexes used in research9分钟
Lecture: Approximate matching, Hamming and edit distance6分钟
Lecture: Pigeonhole principle6分钟
Practical: Implementing the pigeonhole principle 9分钟
1 个阅读材料
Programming Homework 2 Instructions (Read First)10分钟
2 个练习
Module 230分钟
Programming Homework 230分钟
完成时间为 3 小时
Edit distance, assembly, overlaps
This week we finish our discussion of read alignment by learning about algorithms that solve both the edit distance problem and related biosequence analysis problems, like global and local alignment.
完成时间为 3 小时
13 个视频 （总计 92 分钟）, 1 个阅读材料, 2 个测验
13 个视频
Lecture: Solving the edit distance problem12分钟
Lecture: Using dynamic programming for edit distance12分钟
Practical: Implementing dynamic programming for edit distance 6分钟
Lecture: A new solution to approximate matching9分钟
Lecture: Meet the family: global and local alignment10分钟
Practical: Implementing global alignment 8分钟
Lecture: Read alignment in the field4分钟
Lecture: Assembly: working from scratch2分钟
Lecture: First and second laws of assembly8分钟
Lecture: Overlap graphs8分钟
Practical: Overlaps between pairs of reads 4分钟
Practical: Finding and representing all overlaps 3分钟
1 个阅读材料
Programming Homework 3 Instructions (Read First)10分钟
2 个练习
Module 330分钟
Programming Homework 330分钟
完成时间为 3 小时
Algorithms for assembly
In the last module we began our discussion of the assembly problem and we saw a couple basic principles behind it. In this module, we'll learn a few ways to solve the alignment problem.
完成时间为 3 小时
13 个视频 （总计 83 分钟）, 1 个阅读材料, 2 个测验
13 个视频
Lecture: The shortest common superstring problem8分钟
Practical: Implementing shortest common superstring 4分钟
Lecture: Greedy shortest common superstring7分钟
Practical: Implementing greedy shortest common superstring 7分钟
Lecture: Third law of assembly: repeats are bad5分钟
Lecture: De Bruijn graphs and Eulerian walks8分钟
Practical: Building a De Bruijn graph 4分钟
Lecture: When Eulerian walks go wrong9分钟
Lecture: Assemblers in practice8分钟
Lecture: The future is long?9分钟
Lecture: Computer science and life science5分钟
Lecture: Thank yous 43
1 个阅读材料
Post Course Survey10分钟
2 个练习
Programming Homework 430分钟
Module 430分钟
审阅
来自DNA测序算法的热门评论
由 VK 提供Aug 7, 2017
This course provided me a very quick overview of all the core concepts pertaining to DNA sequencing. It is very well organized, crystal clear demonstration of concepts and I really enjoyed the course.
由 KP 提供May 18, 2020
Very good course this is. Just a little advice, please make the quiz questions more clear and more specific because one shouldn't waste time to understand a question which is very easy to implement.
由 MY 提供Oct 9, 2020
One of the most useful courses I have joined. Many thanks to the instructors for these quality lectures and for the time spent to deliver the information as easily as possible!
由 JD 提供Dec 30, 2020
Highly eloquent instructors that make intricate concepts accessible and fun to learn. Would definitely help if you have some programming or bioinformatics background beforehand.
关于 基因组数据科学 专项课程
With genomics sparks a revolution in medical discoveries, it becomes imperative to be able to better understand the genome, and be able to leverage the data and information from genomic datasets. Genomic Data Science is the field that applies statistics and data science to the genome.
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