ongoing Class Notes notes
Ch. 1Sequence AlignmentAlignment Algorithm Overview
9/6 Introduction slides
9/11 Introduction to Sequence Alignment Algorithms slides
9/13Global AlignmentNotes1, Notes2
9/18Global Alignment, Local AlignmentNotes
9/20Local Alignment, Intro to Affine Gap AlignmentNotes
9/30Affine Gap AlignmentNotes Slides
Ch. 2Combinatorial Pattern MatchingKMP and Failure Function Overview
10/04Topological Sort, Intro to Pattern MatchingNotes, Regular Expression Notes
10/09Finite AutomataNotes, Board
10/11More Finite Automata, Failure FunctionNotes
10/16Failure FunctionFF Notes II
10/25Midterm (in class)Midterm topics, Abbreviated Pattern Matching Notes
10/30KMP, Suffix TreesSuffix Trees
Ch. 3Phylogenetic TreesUPGMA and Neighbor-Joining Overview
11/01Intro to Phylogeny, Hora & Tempus ParableThe Parable of the Two Watchmakers
11/06UPGMA AlgorithmNotes
11/13The Neighbor-Joining AlgorithmNotes
11/15The Parsimony Algorithm INotes
11/15The Parsimony Algorithm IINotes
Ch. 4Hidden Markov Models (HMMs)
11/29Introduction to HMMs, Forward AlgorithmNotes I, Notes II, Rabiner HMM Tutorial
12/01Forward Algorithm, Viterbi AlgorithmNotes
Ch. 5Genome Assembly (Intro)
12/11Introduction to Genome AssemblySlides I, Slides II, Slides With Celera Assembler Animation