ongoing |
Class Notes |
notes |

Ch. 1 | Sequence Alignment | Alignment Algorithm Overview |

9/6 |
Introduction |
slides |

9/11 |
Introduction to Sequence Alignment Algorithms |
slides |

9/13 | Global Alignment | Notes1, Notes2 |

9/18 | Global Alignment, Local Alignment | Notes |

9/20 | Local Alignment, Intro to Affine Gap Alignment | Notes |

9/30 | Affine Gap Alignment | Notes Slides |

Ch. 2 | Combinatorial Pattern Matching | KMP and Failure Function Overview |

10/04 | Topological Sort, Intro to Pattern Matching | Notes, Regular Expression Notes |

10/09 | Finite Automata | Notes, Board |

10/11 | More Finite Automata, Failure Function | Notes |

10/16 | Failure Function | FF Notes II |

10/25 | Midterm (in class) | Midterm topics, Abbreviated Pattern Matching Notes |

10/30 | KMP, Suffix Trees | Suffix Trees |

Ch. 3 | Phylogenetic Trees | UPGMA and Neighbor-Joining Overview | |

11/01 | Intro to Phylogeny, Hora & Tempus Parable | The Parable of the Two Watchmakers |

11/06 | UPGMA Algorithm | Notes |

11/13 | The Neighbor-Joining Algorithm | Notes |

11/15 | The Parsimony Algorithm I | Notes |

11/15 | The Parsimony Algorithm II | Notes |

Ch. 4 | Hidden Markov Models (HMMs) | |

11/29 | Introduction to HMMs, Forward Algorithm | Notes I, Notes II, Rabiner HMM Tutorial |

12/01 | Forward Algorithm, Viterbi Algorithm | Notes |

Ch. 5 | Genome Assembly (Intro) | |

12/11 | Introduction to Genome Assembly | Slides I, Slides II,
Slides With Celera Assembler Animation |