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
PDF PPT

Intro. Comp/bio & Bioinformatics Molecular Biology Primer

 Intro 1       (by Matt Ferran)
 Intro 2       (by Anwesha)
Additional Slides: PDF  PPT
Inexact/Approximate Matching
Sequence alignment introduction
& Global Alignment using Dynamic Programming
 Motivation
 Needleman-Wunsch Algorithm
DP algorithm  (by Alireza Ghods) Additional slides: PDF   
Example alignment: PPT

Handbook of Comp. Mol. Bio - Chapter 1
Local Alignment: Smith-Waterman algorithm Motivation 
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
Construction Algorithm & Analysis

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


GENERAL READING AND REFERENCES

    - Here is a good position paper by Sean Eddy about the general direction of computational biology & bioinformatics.

    - A list of course-relevant journals in the area of bioinformatics and computational biology:

            Bioinformatics

            BMC Bioinformatics

            Genome Research

            IEEE/ACM Transactions on Computational Biology and Bioinformatics

            Journal of Computational Biology

            Nucleic Acids Research

            PLoS Computational Biology