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Bioinformatics AlgorithmsAlgorithmsPython ProgrammingAlgorithms On Strings

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1

## DNA sequencing, strings and matching

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
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
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
2

## Preprocessing, indexing and approximate matching

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
3

## Edit distance, assembly, overlaps

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
4

## Algorithms for assembly

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