Tuesday/Thursday 12:30 - 1:45; McBryde 308
CRN: 82197
Instructor: | Lenwood S. Heath |
Office: | 2160J Torgersen Hall |
Email: | heath@vt.edu |
Office Hours: | Tuesday/Thursday 9:00-11:00 |
Graduate Teaching Assistant: | Doaa Altarawy |
Office: | 2160U Torgersen Hall |
Email: | doaa2012@vt.edu |
Office Hours: |
Monday 2:30-3:30
Friday 2:30-4:30 |
Required Text Book:
An Introduction to Bioinformatics Algorithms, by Neil Jones and Pavel Pevzner
Date | Topics | Presenter(s) | Reading | Assignment |
August 25, 27 | Introduction | Heath |
Jones and Pevzner
Chapters 1, 2, 3 |
Homework 1
Due 9/12/2015 |
September 1, 3 |
Exhaustive Search Restriction Mapping Motif Finding |
Heath |
Jones and Pevzner
Chapter 4 |
... |
September 8, 10 | Greedy Algorithms | Heath |
Jones and Pevzner
Chapter 5 |
Homework 2
Due 9/26/2015 |
September 15, 17 |
Dynamic Programming Algorithms
Sequence Comparison and Alignment |
Heath |
Jones and Pevzner
Chapter 6 |
Homework 3
Due 10/10/2015 |
September 22, 24 |
Global Alignment
Local Alignment Discussion of Class Project |
Heath |
Jones and Pevzner
Chapter 6 |
... |
September 29, October 1 |
Combinatorial Pattern Matching | Heath |
Jones and Pevzner
Chapter 9 |
... |
October 6, 8 | Combinatorial Pattern Matching | Heath |
Jones and Pevzner
Chapter 9 |
Homework 4
Due 10/24/2015 |
October 13, 15 | Hidden Markov Models | Heath |
Jones and Pevzner
Chapter 11 |
... |
October 20, 22 |
Structural Biology: The Protein Folding Problem |
Onufriev |
Foldit Online Protein Puzzle; and Foldit Gamers Solve Riddle of HIV Enzyme within 3 Weeks; protein structure lecture; protein folding lecture |
... |
October 27, 29 | Randomized Algorithms | Heath |
Jones and Pevzner
Chapter 12 |
Homework 5
Due 11/14/2015 |
November 3 |
Applications of
Hidden Markov Models |
Zhang |
Lecture notes; Hidden Markov Models and their Applications in Biological Sequence Analysis |
... |
November 5 |
Graph Algorithms
Sequence Assembly |
Heath |
Jones and Pevzner
Chapter 8 |
... |
November 10, 12 | Short Read Mapping | Heath |
How to Map Billions of Short Reads Onto Genomes; and Mapping Reads on a Genomic Sequence |
Homework 6
Due 12/5/2015 |
November 17, 19 | Clustering and Trees | Heath | Jones and Pevzner Chapter 10 |
Tuesday, November 17.
Project presentations, 10 minutes per group. |
December 1, 3 | Clustering and Trees | Heath | Jones and Pevzner Chapter 10 | ... |
December 8 | Wrap up; projects | Heath | ... | December 14. Final project report due by 8:00 AM. |