| 1. | Aug. 27 | Introduction |
| 2. | Aug. 29 | Overview of computational molecular biology and genomics |
| 3. | Sept. 3 | Pairwise sequence comparison - global PS0 handed out - due 9/12 |
| 4. | Sept. 5 | The history of sequencing technology
Guest lecturer:
Dr. Russell
Schwartz No office hours |
| 5. | Sept. 10 | Pairwise sequence comparison - local |
| 6. | Sept. 12 | Multiple sequence alignment - global PS0 due in class |
| 7. | Sept. 17 | Multiple sequence alignment - global |
| 8. | Sept. 19 | Genetic Linkage
and Genomic Evolution, Science2002, registration. Alumni Hall (formerly Masonic Temple, across 5th avenue from the Cathedral of Learning), 7th floor Auditorium. |
| 9. | Sept. 24 | Multiple sequence alignment - local Online protein domain databases: PS1 handed out - due 10/1 Alignment template |
| 10. | Sept. 26 | Multiple sequence alignment - local Hidden Markov Models (HMMs), Guest lecturer: Dr. William Cohen |
| 11. | Oct. 1 | Multiple sequence alignment - local HMMs continued, Guest lecturer: Dr. William Cohen PS1 due in class |
| 12. | Oct. 3 | Applications of HMMs to molecular biology: CpG islands,
profile HMM's for modeling domains, multiple sequence alignment PS2 handed out - due 10/10 Matrix template |
| 13. | Oct. 8 | Substitution matrices Likelihood ratios, PAM matrices PAM250, BLOSUM62 |
| 14. | Oct. 10 | Substitution matrices continued PAM and BLOSUM matrices Lecture outline PS2 due in class |
| 15. | Oct. 15 | Midterm Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. The midterm covers all material up to and including biological applications of HMM's. |
| 16. | Oct. 17 | Review of midterm. Introduction to class projects for 03-711 |
| 17. | Oct. 22 | Database searching; BLAST BLAST home page Lecture outline |
| 18. | Oct. 24 | Blast; statistics of local, ungapped alignments. Lecture outline |
| 19. | Oct. 29 | Gapped Blast; Blast demo. Lecture outline |
| 20. | Oct. 31 | Phylogeny reconstruction Lecture outline PS3 handed out - due 11/12 Project proposal/outlines due. |
| 21. | Nov. 5 | Phylogeny reconstruction: parsimony Lecture outline |
| 22. | Nov. 7 | Phylogeny reconstruction: distance-based methods Lecture outline |
| 23. | Nov. 12 | Phylogeny reconstruction: distance-based methods Lecture outline UPGMA algorithm NJ algorithm Revised project proposal/outlines due. PS3 due in class |
| 24. | Nov. 14 | No class |
| 25. | Nov. 19 | Phylogeny reconstruction: maximum likelihood Lecture outline Comparison of tree reconstruction algorithms |
| 26. | Nov. 21 | Gene Finding (prokaryotic) Lecture outline PS4 handed out - due 12/03 |
| 27. | Nov. 26 | Gene Finding (eukaryotic) Lecture outline Gene Prediction in the Human Genome Project No office hours. |
| Nov. 28 | Thanksgiving-no class | |
| 28. | Dec. 3 | Project
presentations PS4 due in class |
| 29. | Dec. 5 |
Project presentations 10:30 - 10:40 Course evaluation Project final papers due. |
| 30. | Monday Dec. 9 |
Final Exam: 8:30 - 11:30 Porter Hall A18A This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Bring a calculator. The final exam is cummulative. You are responsible for all material covered during the semester. |