| Date |
Topic of Lecture |
Reading Material |
Assignment |
| Jan. 8, 10, and 17 |
Lecture 1: Introduction
 |
Introduction to
Bioinformatics
|
|
Databases and How to Query Them
|
|
|
Read material by 1/10 Go through tutorial by
1/12
|
| Jan
12 |
Lab
Day |
|
Obtain Software needed for
course |
|
Literature Queries |
|
|
| Jan
19 |
Lab
Day |
|
Obtain Software needed for
course |
| Database queries (protein and
gene) |
|
Assignment
1 due 1/26 |
| January 22 and 24 |
Lecture 2A: Molecular
Biology Tools (Primer Design software, Restriction mapping software,
PCR, Sequencing) |
| Chapter 1 (your Bioinformatics Text) |
|
Read Material by
Jan. 22
|
| Jan
26 |
Lab
Day |
|
Primer Design, Restriction
Mapping |
|
Assignment
2 due 2/2 |
| Jan. 29, 31 and Feb. 2 |
Lecture 2B: Review of Molecular Biology and Biological Chemistry
Student directed lectures!
|
| Chapter 1
|
|
Be Prepared to give your presentation on
1/29 |
| Feb. 5 |
Elements of an oral
presentation
|
|
|
| Feb. 5, 7,
9 |
Lecture 3A: Pairwise Alignment and Homology
|
| Chapter 2 |
|
|
| Feb.
9 |
Lab
Day |
|
Dot Plots |
|
Scoring Alignments |
|
Assignment
3 due
2/19 |
| Feb. 12, 14 |
Lecture 3B: Pairwise Alignment and Blast
|
|
|
| Feb.
16 |
Lab
Day |
|
Partial Scores Tables |
|
BLAST Searches |
|
Assignment
4 due
2/19 |
| Feb. 19, 21, |
Lecture
4: Substitution Patterns and Multiple Sequence Alignment |
|
Chapter 3
|
|
|
| Feb.
23 |
Midterm (Lectures
1-4)
|
| Feb.
23-27 |
Midterm
Grades Posted in Duck
|
| March
2 |
Last Day to Drop
Without Academic Penalty
|
| Feb. 26, 28, March 2,
12 |
Lecture 5: Phylogeny |
|
|
| March
14 and 16 |
Lab
Days |
|
Multiple Sequence Alignments |
|
Distance-Based Phylogenetic Trees |
|
Parsimony (optimality)-based Phylogenetic Trees |
|
Assignment
5 due |
| March 19, 21 |
Lecture 6A: Genomics and Gene
Recognition |
| Chapter 6 |
|
|
| March
23 |
Lab
Day |
|
Locating Genes in Prokaryotic Genomes |
|
Assignment
6 due |
| March 26, 28 |
Lecture 6B: Genomics and Gene Recognition |
| Chapter 6 |
|
|
| March
30 |
Lab
Day |
|
Genomic Mapping |
|
Locating Genes in Eukaryotic Genomes |
|
Assignment
7 due |
| April 2, 4 |
Lecture 7A: Protein Structure Prediction and Proteomics |
|
|
| April
6 |
Lab
Day |
|
Secondary Structure Prediction |
|
Protein Domain Prediction |
|
Assignment
8 due |
| April 9, 11 |
Lecture 7B: Protein Structure Prediction and Modeling and
Proteomics |
|
|
| April
13, 16 |
Lab
Days |
|
Protein Structure Modeling |
|
Assignment
9 due |
| April 18, 20 |
Finish
Lecture 7 and tie up loose ends |
|
|
| April
23 |
Lab
Day |
|
Project Work |
|
|
| April
25, 27 and 30 |
Student Project
Presentations
|
| 5/2/07 |
Final Exam
7:30 a.m. to 9:30 a.m.
(Cumulative--Lectures 1-8)
|