课程信息
4.8
351 个评分
86 个审阅
专项课程
100% 在线

100% 在线

立即开始,按照自己的计划学习。
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完成时间(小时)

完成时间大约为21 小时

建议:7 hours/week...
可选语言

英语(English)

字幕:英语(English)

您将获得的技能

Bioinformatics AlgorithmsAlgorithmsPython ProgrammingAlgorithms On Strings
专项课程
100% 在线

100% 在线

立即开始,按照自己的计划学习。
可灵活调整截止日期

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(小时)

完成时间大约为21 小时

建议:7 hours/week...
可选语言

英语(English)

字幕:英语(English)

教学大纲 - 您将从这门课程中学到什么

1
完成时间(小时)
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. ...
Reading
19 个视频 (总计 112 分钟), 7 个阅读材料, 2 个测验
Video19 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
Reading7 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
Quiz2 个练习
Module 120分钟
Programming Homework 114分钟
2
完成时间(小时)
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...
Reading
15 个视频 (总计 114 分钟), 1 个阅读材料, 2 个测验
Video15 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
Reading1 个阅读材料
Programming Homework 2 Instructions (Read First)10分钟
Quiz2 个练习
Module 220分钟
Programming Homework 212分钟
3
完成时间(小时)
完成时间为 2 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....
Reading
13 个视频 (总计 92 分钟), 1 个阅读材料, 2 个测验
Video13 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
Reading1 个阅读材料
Programming Homework 3 Instructions (Read First)10分钟
Quiz2 个练习
Module 320分钟
Programming Homework 38分钟
4
完成时间(小时)
完成时间为 2 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....
Reading
13 个视频 (总计 83 分钟), 1 个阅读材料, 2 个测验
Video13 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 分钟
Reading1 个阅读材料
Post Course Survey10分钟
Quiz2 个练习
Programming Homework 48分钟
Module 414分钟
4.8
86 个审阅Chevron Right
职业方向

33%

完成这些课程后已开始新的职业生涯
工作福利

83%

通过此课程获得实实在在的工作福利

热门审阅

创建者 VKAug 8th 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.

创建者 MDNov 10th 2016

This was really fun. Really enjoyed the a-ha of the algorithms and the fun of solving the alignment and assembly problems. Feel mildly powerful after assembling a virus genome.

讲师

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Ben Langmead, PhD

Assistant Professor
Computer Science
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Jacob Pritt

Department of Computer Science

关于 Johns Hopkins University

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....

关于 Genomic Data Science 专项课程

This specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, Python, R, Bioconductor, and Galaxy. The sequence is a stand alone introduction to genomic data science or a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics. To audit Genomic Data Science courses for free, visit https://www.coursera.org/jhu, click the course, click Enroll, and select Audit....
Genomic Data Science

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