| Topic |
Date |
Remarks |
| Introduction: comparison of DNA sequences, Perl and Python |
01/18/11 |
Slides |
| Comparing DNA sequences |
01/20/11 |
|
| Class cancelled and will be rescheduled |
01/25/11 |
|
| Class cancelled due to weather |
01/27/11 |
|
| Basic Python exercises for DNA analysis |
02/01/11 |
Sequence alignment notes HW 1 |
| Affine gaps and traceback | 02/03/11 |
HW 2 |
| Scoring alignments using affine gaps and random traceback | 02/08/11 |
HW 3 |
| Random alignments |
02/10/11 |
HW 4 |
| Optimal sequence alignment: computing scoring
matrix V |
02/15/11 |
HW 5 |
| Optimal sequence alignment, functions, and
modules |
02/17/11 |
HW 6 |
| Optimal sequence alignment |
02/22/11 |
HW 7 |
| Optimal sequence alignment |
02/24/11 |
HW 8 |
| Finding similar sequences |
03/01/11 |
dna_fasta.txt query.txt HW 9 |
| Local alignment and running time issues |
03/03/11 |
HW 10 |
| Alignment and review |
03/08/11 |
|
| First exam | 03/10/11 |
|
| Spring break | 03/15/11 |
|
| Spring break | 03/17/11 |
|
| Distance based phylogeny reconstruction, UPGMA | 03/22/11 |
Slides HW 11 |
| UPGMA | 03/24/11 | HW 12 |
| UPGMA | 03/29/11 | HW 13 |
| Lecture by Zhi Wei | 03/31/11 |
|
| UPGMA in Python | 04/05/11 |
HW 14 |
| UPGMA in Python | 04/07/11 |
HW 15 |
| UPGMA in Python and newick format for trees | 04/12/11 |
|
| UPGMA in Python | 04/14/11 |
HW 16 |
| UPGMA in Python | 04/19/07 |
|
| Second exam | 04/21/11 |
|
| Solution to exam and extra-credit assignment | 04/26/11 |
Extra credit assignment README |
| Neighbor joining (NJ) in Python | 04/28/11 |
|
| NJ in Python | 05/04/11 |
|
| Final exam | 05/09/11 |