關於此課程：我们将学会对 DNA 测序数据进行分析的计算方法——算法和数据结构。我们将学习一点DNA、基因组、以及 DNA 测序的应用的相关知识。我们将使用 Python 实现关键算法和数据结构，并分析实际的基因组和 DNA 测序数据集。
製作方： Johns Hopkins University
教學方： Ben Langmead, PhD, Assistant Professor
Computer Science
教學方： Jacob Pritt
Department of Computer Science
| 基本信息 | 課程 4（共 8 門，基因组数据科学 Specialization ） |
| 語言 | English |
| 如何通過 | 通過所有計分作業以完成課程。 |
| 用戶評分 |
授課大綱
第 1 週
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.
19 個視頻, 7 個閱讀材料
- Reading: Welcome to Algorithms for DNA Sequencing
- Reading: Pre Course Survey
- Reading: Syllabus
- Reading: Setting up Python (and Jupyter)
- Reading: Getting slides and notebooks
- Reading: Using data files with Python programs
- 視頻: Lecture: Why study this?
- 視頻: Lecture: DNA sequencing past and present
- 視頻: Lecture: Genomes as strings, reads as substrings
- 視頻: Lecture: String definitions and Python examples
- 視頻: Practical: String basics
- 視頻: Practical: Manipulating DNA strings
- 視頻: Practical: Downloading and parsing a genome
- 視頻: Lecture: How DNA gets copied
- 視頻: Optional lecture: How second-generation sequencers work
- 視頻: Optional lecture: Sequencing errors and base qualities
- 視頻: Lecture: Sequencing reads in FASTQ format
- 視頻: Practical: Working with sequencing reads
- 視頻: Practical: Analyzing reads by position
- 視頻: Lecture: Sequencers give pieces to genomic puzzles
- 視頻: Lecture: Read alignment and why it's hard
- 視頻: Lecture: Naive exact matching
- 視頻: Practical: Matching artificial reads
- 視頻: Practical: Matching real reads
- Reading: Programming Homework 1 Instructions (Read First)
已評分: Module 1
已評分: Programming Homework 1
第 2 週
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
15 個視頻, 1 個閱讀材料
- 視頻: Lecture: Boyer-Moore basics
- 視頻: Lecture: Boyer-Moore: putting it all together
- 視頻: Lecture: Diversion: Repetitive elements
- 視頻: Practical: Implementing Boyer-Moore
- 視頻: Lecture: Preprocessing
- 視頻: Lecture: Indexing and the k-mer index
- 視頻: Lecture: Ordered structures for indexing
- 視頻: Lecture: Hash tables for indexing
- 視頻: Practical: Implementing a k-mer index
- 視頻: Lecture: Variations on k-mer indexes
- 視頻: Lecture: Genome indexes used in research
- 視頻: Lecture: Approximate matching, Hamming and edit distance
- 視頻: Lecture: Pigeonhole principle
- 視頻: Practical: Implementing the pigeonhole principle
- Reading: Programming Homework 2 Instructions (Read First)
已評分: Module 2
已評分: Programming Homework 2
第 3 週
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.
13 個視頻, 1 個閱讀材料
- 視頻: Lecture: Solving the edit distance problem
- 視頻: Lecture: Using dynamic programming for edit distance
- 視頻: Practical: Implementing dynamic programming for edit distance
- 視頻: Lecture: A new solution to approximate matching
- 視頻: Lecture: Meet the family: global and local alignment
- 視頻: Practical: Implementing global alignment
- 視頻: Lecture: Read alignment in the field
- 視頻: Lecture: Assembly: working from scratch
- 視頻: Lecture: First and second laws of assembly
- 視頻: Lecture: Overlap graphs
- 視頻: Practical: Overlaps between pairs of reads
- 視頻: Practical: Finding and representing all overlaps
- Reading: Programming Homework 3 Instructions (Read First)
已評分: Module 3
已評分: Programming Homework 3
第 4 週
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.
13 個視頻, 1 個閱讀材料
- 視頻: Lecture: The shortest common superstring problem
- 視頻: Practical: Implementing shortest common superstring
- 視頻: Lecture: Greedy shortest common superstring
- 視頻: Practical: Implementing greedy shortest common superstring
- 視頻: Lecture: Third law of assembly: repeats are bad
- 視頻: Lecture: De Bruijn graphs and Eulerian walks
- 視頻: Practical: Building a De Bruijn graph
- 視頻: Lecture: When Eulerian walks go wrong
- 視頻: Lecture: Assemblers in practice
- 視頻: Lecture: The future is long?
- 視頻: Lecture: Computer science and life science
- 視頻: Lecture: Thank yous
- Reading: Post Course Survey
已評分: Programming Homework 4
已評分: Module 4
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製作方
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.
價格
| 購買課程 | |
|---|---|
| 訪問課程材料 | 可用 |
| 訪問評分的材料 | 可用 |
| 收到最終成績 | 可用 |
| 獲得可共享的課程證書 | 可用 |
評分和審閱
Very well prepared, from basics up to all commonly used techniques in bioinformatics. Prerequisites in Python is a plus, but not even necessary.
it's really a helpful course, and it would show you the basic algorithms of the software we are using today.
Good course, well presented. There was some linking with the underlying biology though I would have liked more of this. Even though the course is essentially about generic string processing algorithms, it needs to be kept focused on the genomics - which mostly it was.
It is well explained. More space to programming practical exercise is suggested.Very intriguing Programming Homework! You have to apply all the python knowledge you have learned so far and also the one you have still to learn :)