Ch. 1Sequence AlignmentAlignment Algorithm Overview
9/07Course introductionSlides, Dancing Man
9/12Introduction to AlignmentNotes, Slides
9/14Global AlignmentNotes
9/19Global Alignment, Local AlignmentNotes
9/21Local Alignment, Intro to Affine Gap AlignmentNotes
9/26Affine Gap AlignmentNotes
Ch. 2Combinatorial Pattern MatchingKMP and Failure Function Overview
9/28Topological Sort, Intro to Pattern MatchingNotes, Regular Expression Notes
10/03Finite AutomataNotes, Board
10/05More Finite Automata, Failure FunctionNotes
10/10Failure FunctionFF Notes II
10/12Guest LectureDistinguished Lecture , Article I, Article II
10/17KMP, Suffix TreesSuffix Trees
Ch. 3Phylogenetic TreesUPGMA and Neighbor-Joining Overview
10/19Intro to Phylogeny, Hora & Tempus ParableThe Parable of the Two Watchmakers
10/26Midterm (in class)Midterm topics, Abbreviated Pattern Matching Notes
10/31UPGMA AlgorithmNotes
11/02The Neighbor-Joining AlgorithmNotes
11/07The Parsimony Algorithm INotes
11/09The Parsimony Algorithm IINotes
11/14Hora and Tempus
Ch. 4Hidden Markov Models (HMMs)
11/16Introduction to HMMs, Forward AlgorithmNotes I, Notes II, Rabiner HMM Tutorial
11/21Forward Algorithm, Viterbi AlgorithmNotes
11/23No class (Thanksgiving)
11/28The Viterbi algorithm for decoding
Ch. 5Genome Assembly (Intro)
11/30Introduction to Genome AssemblySlides I, Slides II
12/12More Genome Assembly
12/15Final Exam (posted online)Final Exam Topics