Topic
|
Date
|
Remarks
|
Pairwise sequence alignment
|
08/31/10
|
|
Perl basics and sequence analysis exercises in Perl
|
09/07/10
|
|
Optimal sequence alignment in Perl, affine gaps,
and subroutines in Perl
|
09/14/10
|
|
| Affine gap sequence alignment, local alignment and
BLAST, alignment accuracy
|
09/21/10
|
|
Alignment papers; Review
|
09/28/10
|
|
First mid-term
|
10/05/10
|
|
Perl exercises and more alignment
|
10/12/10
|
|
Hidden Markov models (HMM) for sequence alignment
|
10/19/10
|
|
HMMs for sequence alignment and BLAST exercise
|
10/26/10
|
|
| Expected accuracy alignment and review for second exam
|
11/02/10
|
|
| Second exam, SNPs, and population structure identification
|
11/09/10
|
|
PCA and k-means
|
11/16/10
|
|
K-means clustering in Perl
|
11/23/09
|
|
Extra credit assignment and review
|
11/30/09
|
|
Final exam
|
12/14/10
|
|