About this course: 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。
Created by: 约翰霍普金斯大学
Taught by: Ben Langmead, PhD, Assistant Professor
Computer Science
Taught by: Jacob Pritt
Department of Computer Science
| Basic Info | Course 4 of 8 in the 基因组数据科学 Specialization |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
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 videos, 7 readings
- 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
- Video: Lecture: Why study this?
- Video: Lecture: DNA sequencing past and present
- Video: Lecture: Genomes as strings, reads as substrings
- Video: Lecture: String definitions and Python examples
- Video: Practical: String basics
- Video: Practical: Manipulating DNA strings
- Video: Practical: Downloading and parsing a genome
- Video: Lecture: How DNA gets copied
- Video: Optional lecture: How second-generation sequencers work
- Video: Optional lecture: Sequencing errors and base qualities
- Video: Lecture: Sequencing reads in FASTQ format
- Video: Practical: Working with sequencing reads
- Video: Practical: Analyzing reads by position
- Video: Lecture: Sequencers give pieces to genomic puzzles
- Video: Lecture: Read alignment and why it's hard
- Video: Lecture: Naive exact matching
- Video: Practical: Matching artificial reads
- Video: Practical: Matching real reads
- Reading: Programming Homework 1 Instructions (Read First)
Graded: Module 1
Graded: Programming Homework 1
WEEK 2
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 videos, 1 reading
- Video: Lecture: Boyer-Moore basics
- Video: Lecture: Boyer-Moore: putting it all together
- Video: Lecture: Diversion: Repetitive elements
- Video: Practical: Implementing Boyer-Moore
- Video: Lecture: Preprocessing
- Video: Lecture: Indexing and the k-mer index
- Video: Lecture: Ordered structures for indexing
- Video: Lecture: Hash tables for indexing
- Video: Practical: Implementing a k-mer index
- Video: Lecture: Variations on k-mer indexes
- Video: Lecture: Genome indexes used in research
- Video: Lecture: Approximate matching, Hamming and edit distance
- Video: Lecture: Pigeonhole principle
- Video: Practical: Implementing the pigeonhole principle
- Reading: Programming Homework 2 Instructions (Read First)
Graded: Module 2
Graded: Programming Homework 2
WEEK 3
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 videos, 1 reading
- Video: Lecture: Solving the edit distance problem
- Video: Lecture: Using dynamic programming for edit distance
- Video: Practical: Implementing dynamic programming for edit distance
- Video: Lecture: A new solution to approximate matching
- Video: Lecture: Meet the family: global and local alignment
- Video: Practical: Implementing global alignment
- Video: Lecture: Read alignment in the field
- Video: Lecture: Assembly: working from scratch
- Video: Lecture: First and second laws of assembly
- Video: Lecture: Overlap graphs
- Video: Practical: Overlaps between pairs of reads
- Video: Practical: Finding and representing all overlaps
- Reading: Programming Homework 3 Instructions (Read First)
Graded: Module 3
Graded: Programming Homework 3
WEEK 4
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 videos, 1 reading
- Video: Lecture: The shortest common superstring problem
- Video: Practical: Implementing shortest common superstring
- Video: Lecture: Greedy shortest common superstring
- Video: Practical: Implementing greedy shortest common superstring
- Video: Lecture: Third law of assembly: repeats are bad
- Video: Lecture: De Bruijn graphs and Eulerian walks
- Video: Practical: Building a De Bruijn graph
- Video: Lecture: When Eulerian walks go wrong
- Video: Lecture: Assemblers in practice
- Video: Lecture: The future is long?
- Video: Lecture: Computer science and life science
- Video: Lecture: Thank yous
- Reading: Post Course Survey
Graded: Programming Homework 4
Graded: Module 4
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Ratings and Reviews
I loved this course. The material was really interesting and it was well taught. The assignments were excellent as well.
Very good lectures. Some of the homework assignments were kind of hard though (and no help in the discussion forums).
Helpful material for DNA Sequencing and number crunching.
Well taught, I suggest a background in Python to make things more enjoyable.
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I enjoyed the introduction to some of the algorithms used in genomics... and hope to explore these further in my career.