| Topic |
Date |
Remarks |
| Introduction: Python |
01/22/13 |
|
| Comparing DNA sequences | 01/25/13 |
Slides HW 1 |
| Sequence alignment | 01/29/13 |
Alignment notes HW 2 |
| Random traceback to compute random alignments | 02/01/13 |
Affine gaps HW 3 |
| Functions and random traceback | 02/05/13 |
HW 4 |
| Class cancelled due to storm | 02/08/13 |
|
| Needleman-Wunsch | 02/12/13 |
Needleman-Wunsch slides HW 5 |
| Needleman-Wunsch | 02/15/13 |
|
| Needleman-Wunsch | 02/19/13 |
HW 6 |
| Needleman-Wunsch | 02/22/13 |
HW 7 |
| Finding similar sequences in a database |
02/26/13 |
HW 8 |
| Finding similar sequences in a database |
03/01/13 |
Horse Haemoglobin (PDB 2dhb) Sequences from BLAST search BLAST output Chicken Cytochrome bc 1 (PDB 3h1j) Sequences from BLAST searh BLAST output |
| 03/05/13 |
||
| First exam |
03/08/13 |
|
| Exam solution and database search |
03/12/13 |
HW 9 |
| Running time analysis and BLAST-like database search |
03/15/13 |
HW 10 BLOSUM_62 matrix |
| Spring break | 03/19/13 |
|
| Spring break | 03/22/13 |
|
| Fast BLAST-like search, genome database search, Smith-Waterman local alignment, distance based phylogeny reconstruction, UPGMA | 03/26/13 |
Smith-Waterman alignment slides E.coli K12 MG1655 genome Related proteobacteria genomes Bacterial phylogeny UPGMA |
| Good Friday | 03/29/13 |
|
| Distance based phylogeny reconstruction, UPGMA | 04/02/13 |
UPGMA |
| UPGMA algorithm, data structure to represent phylogenies | 04/05/13 |
|
| UPGMA implementation in Python | 04/09/13 |
UPGMA implementation Python function to make Newick tree HW 11 |
| UPGMA implementation in Python | 04/12/13 |
HW 12 |
| UPGMA implementation in Python | 04/16/13 | HW 13 |
| UPGMA implementation in Python | 04/19/13 |
Haemoglobin sequences (SWISSPROT species IDs) ClustalW webserver Haemoglobin aligned sequences Jukes Cantor distance matrix for Haemoglobin aligned sequences Online phylogeny viewer |
| UPGMA in Python, review | 04/23/13 | Jukes Cantor distances |
| Second exam | 04/26/13 |
|
| Calculating distance matrices and UPGMA trees from unaligned sequences | 04/30/13 |
Extra credit assignment |
| Neighbor joining algorithm | 05/03/13 |
Neighbor joining |
| Review for final | 05/07/13 |
|
| Final exam | 05/15/13 |
8:30-11am in room FMH 404 |
