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Bioinformatics AlgorithmsAlgorithmsPython ProgrammingAlgorithms On Strings

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1

## DNA sequencing, strings and matching

19 個視頻 （總計 112 分鐘）, 7 個閱讀材料, 2 個測驗
19 個視頻
Lecture: Why study this?4分鐘
Lecture: DNA sequencing past and present3分鐘
Lecture: Genomes as strings, reads as substrings5分鐘
Lecture: String definitions and Python examples3分鐘
Practical: String basics 7分鐘
Practical: Manipulating DNA strings 7分鐘
Lecture: How DNA gets copied3分鐘
Optional lecture: How second-generation sequencers work 7分鐘
Optional lecture: Sequencing errors and base qualities 6分鐘
Lecture: Sequencing reads in FASTQ format4分鐘
Practical: Working with sequencing reads 11分鐘
Practical: Analyzing reads by position 6分鐘
Lecture: Sequencers give pieces to genomic puzzles5分鐘
Lecture: Read alignment and why it's hard3分鐘
Lecture: Naive exact matching10分鐘
7 個閱讀材料
Welcome to Algorithms for DNA Sequencing10分鐘
Pre Course Survey10分鐘
Syllabus10分鐘
Setting up Python (and Jupyter)10分鐘
Getting slides and notebooks10分鐘
Using data files with Python programs10分鐘
Programming Homework 1 Instructions (Read First)10分鐘
2 個練習
Module 130分鐘
Programming Homework 130分鐘
2

## Preprocessing, indexing and approximate matching

15 個視頻 （總計 114 分鐘）, 1 個閱讀材料, 2 個測驗
15 個視頻
Lecture: Boyer-Moore basics8分鐘
Lecture: Boyer-Moore: putting it all together6分鐘
Lecture: Diversion: Repetitive elements5分鐘
Practical: Implementing Boyer-Moore 10分鐘
Lecture: Preprocessing7分鐘
Lecture: Indexing and the k-mer index10分鐘
Lecture: Ordered structures for indexing8分鐘
Lecture: Hash tables for indexing7分鐘
Practical: Implementing a k-mer index 7分鐘
Lecture: Variations on k-mer indexes9分鐘
Lecture: Genome indexes used in research9分鐘
Lecture: Approximate matching, Hamming and edit distance6分鐘
Lecture: Pigeonhole principle6分鐘
Practical: Implementing the pigeonhole principle 9分鐘
1 個閱讀材料
Programming Homework 2 Instructions (Read First)10分鐘
2 個練習
Module 230分鐘
Programming Homework 230分鐘
3

## Edit distance, assembly, overlaps

13 個視頻 （總計 92 分鐘）, 1 個閱讀材料, 2 個測驗
13 個視頻
Lecture: Solving the edit distance problem12分鐘
Lecture: Using dynamic programming for edit distance12分鐘
Practical: Implementing dynamic programming for edit distance 6分鐘
Lecture: A new solution to approximate matching9分鐘
Lecture: Meet the family: global and local alignment10分鐘
Practical: Implementing global alignment 8分鐘
Lecture: Read alignment in the field4分鐘
Lecture: Assembly: working from scratch2分鐘
Lecture: First and second laws of assembly8分鐘
Lecture: Overlap graphs8分鐘
Practical: Overlaps between pairs of reads 4分鐘
Practical: Finding and representing all overlaps 3分鐘
1 個閱讀材料
Programming Homework 3 Instructions (Read First)10分鐘
2 個練習
Module 330分鐘
Programming Homework 330分鐘
4

## Algorithms for assembly

13 個視頻 （總計 83 分鐘）, 1 個閱讀材料, 2 個測驗
13 個視頻
Lecture: The shortest common superstring problem8分鐘
Practical: Implementing shortest common superstring 4分鐘
Lecture: Greedy shortest common superstring7分鐘
Practical: Implementing greedy shortest common superstring 7分鐘
Lecture: Third law of assembly: repeats are bad5分鐘
Lecture: De Bruijn graphs and Eulerian walks8分鐘
Practical: Building a De Bruijn graph 4分鐘
Lecture: When Eulerian walks go wrong9分鐘
Lecture: Assemblers in practice8分鐘
Lecture: The future is long?9分鐘
Lecture: Computer science and life science5分鐘
Lecture: Thank yous 43
1 個閱讀材料
Post Course Survey10分鐘
2 個練習
Programming Homework 430分鐘
Module 430分鐘