| Week 1 | Course description and introduction to molecular biology. |
| Week 2 | Introduction to molecular biology. Sequence alignment. |
| Week 3 | No class on Monday (9/1) - Labor day. Alignment types. Edit distance. Needleman-Wunsch method. |
| Week 4 | Linear space methods. Scoring measures. Banded alignment. Local alignment. Dovetail alignment. Pattern search. Non-overlapping alignments. |
| Week 5 | Gap models. Protein structures. |
| Week 6 | Protein structures. |
| Week 7 |
Project proposal due Wednesday
(10/01). Structure prediction |
| Week 8 | Substitution matrices |
| Week 9 | Heuristics alignment No class on Friday (10/17) - Homecoming. |
| Week 10 | Statistical significance of alignment. Phylogenetic trees. |
| Week 11 | Phylogenetic tree construction. Consensus trees. |
| Week 12 | Multiple sequence alignment |
| Week 13 | Multiple sequence alignment |
| Week 14 |
Biological networks
|
| Week 15 | No classes - Thanksgiving. |
| Week 16 |
Sequence assembly. Wrap up semester.
Project report is due (12/5). |