| Topic |
Date |
Remarks |
| Introduction |
09/04/07 |
Slides |
| Perl |
09/11/07 |
Slides Basic Unix command sheet |
| Computing alignment score in Perl |
09/18/07 |
score.pl |
| Subroutines, returning arrays and hashes, and sequence alignment in Perl |
09/25/07 |
Slides |
| Affine gaps |
10/02/07 |
Affine gaps |
| Comparing alignments and training |
10/09/07 |
Alignment notes |
| Mid-term exam |
10/16/07 |
|
| Mid-term solution, parameter optimization |
10/23/07 |
BLOSUM 62 PREFAB pairwise alignments |
| Parameter optimization |
10/30/07 |
simple matrix training datasets testing datasets |
| Hidden Markov models, parameter estimation |
11/06/07 |
Slides HMM notes |
| Hidden Markov models in Perl |
11/13/07 |
gen_loadeddie.pl |
| Thanksgiving break -- no class |
11/20/07 |
|
| HMM pairwise alignment in Perl, profile alignment |
11/27/07 |
match/mismatch emission probabilities (blosum62.qij) HMM probabilities from Probcons program Slides |
| Local alignment, BLAST |
12/04/07 |
Slides |