| Week 1 | Course description and introduction to molecular biology. |
| Week 2 | Introduction to molecular biology. Sequence alignment. |
| Week 3 | No class on Monday (9/2) - 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 Friday
(10/04). Structure prediction |
| Week 8 | Substitution matrices |
| Week 9 | Heuristics alignment No class on Friday (10/18) - Homecoming. |
| Week 10 | Statistical significance of alignment. Phylogenetic trees. |
| Week 11 | Phylogenetic tree construction. Consensus trees. |
| Week 12 | Multiple sequence alignment |
| Week 13 | No class on Monday (11/11) - Veterans day. |
| Week 14 |
Multiple sequence alignment
|
| Week 15 | No classes - Thanksgiving. |
| Week 16 |
Project presentations (1
day1)
Project report is due (12/7). |