Cpt S 471/571:    LECTURE NOTES

PDF links to lecture notes will be updated as the course progresses.

 Topic Instructor Scribes/Lecture Notes Student Scribes Other References Course introduction Intro. Comp/bio & Bioinformatics Intro 1       (by Matt Ferran)  Intro 2       (by Anwesha) Additional Slides: PDF  PPT Inexact/Approximate Matching Sequence alignment introduction & Global Alignment using Dynamic Programming DP algorithm  (by Alireza Ghods) Additional slides: PDF    Example alignment: PPT Handbook of Comp. Mol. Bio - Chapter 1 Local Alignment: Smith-Waterman algorithm SW algorithm (by Wilson Garrett) Handbook of Comp. Mol. Bio - Chapter 1 Alignment with Affine Gap Penalty function Motivation   Algorithm Affine Gap intro (by Biresh) Affine Gap algorithm (by Bhavesh) Handbook of Comp. Mol. Bio - Chapter 1 Semi-Global algorithm Motivation   Algorithm Algorithm (by Priyank) Space-Optimal Global Alignment (linear space) The Hirschberg Technique Part 1  Part 2 Algorithm (by Christian Francisco) K-band algorithm Algorithm and analysis Algorithm (by MinShi) Edit Distance Definition and Algorithm Exact Matching Exact Matching overview Application motivation Look-up tables Handbook of Comp. Mol. Bio - Chapter 5 BLAST Algorithm      PPT PDF Handbook of Comp. Mol. Bio - Chapter 5 String "Trie" data structures Tries and compacted tries Tries intro (by Kaniz Madhobi) PATRICIA trees (by Kaniz Madhobi) Handbook of Comp. Mol. Bio - Chapter 5 Suffix Tree  data structure Definition , properties & examples Suffix tree intro (by Deepesh) Handbook of Comp. Mol. Bio - Chapter 5,6 Suffix Trees: Basic Applications Applications:   Longest repeat,    Pattern matching,   Longest common substring Handbook of Comp. Mol. Bio - Chapter 5,6 Suffix Trees: Construction Suffix Links & McCreight's algorithm (1976): Main idea (algorithm summary) Detailed algorithm Example (for worst-case input) slides: PPT   PDF Handbook of Comp. Mol. Bio - Chapter 5,6 Lowest Common Ancestor Algorithm Bender-Farach algorithm  - Class lecture scribe - Detailed notes Handbook of Comp. Mol. Bio - Chapter 5,6 Suffix Trees: More Applications Restriction enzyme site detection RNAi (gene silencing) detection Prefix-Suffix/superstring Maximal matching Handbook of Comp. Mol. Bio - Chapters 5,6 Read Mapping (Project 3) Class scribe Suffix Arrays and Burrows Wheeler Transform (BWT) Handbook of Comp. Mol. Bio - Chapter 7 Probabilistic Modeling for Biological Sequence Analysis Probabilistic Modeling, Markov Chains Introduction to Probabilistic modeling & Markov Chains Durbin et al. - Chapters 1-4 Hidden Markov Models (HMMs) HMMs, Viterbi's decoding Durbin et al. - Chapters 1-4 HMM algorithms: decoding, forward and backward Durbin et al. - Chapters 1-4 Genome-scale problems Genome assembly: algorithms and data structures Handbook of Comp. Mol. Bio - Chapters 8,9, 13 Phylogenetic tree reconstruction Gusfield - Chapter 17