| √ |
|
What |
|
When |
Who |
| √ |
Lecture 1 |
Basics,Sequencing, edit distance |
PDF |
Aug 30, 2004 |
Chris |
| √ |
Lecture 2 |
Databases, Dotplots |
PDF |
Sep 2, 2004 |
Chris |
| √ |
Lecture 3 |
Pairwise sequence alignment without gaps |
PDF |
Sep 9, 2004 |
Chris |
| √ |
Lecture 4 |
Gapped alignment, dynamic programming |
PDF |
Sep 13, 2004 |
Chris |
| √ |
Lecture 5 |
Affine gap penalties, Local versus global |
PDF |
Sep 16, 2004 |
Chris |
| &radic |
Lecture 6 |
Substitution matrices |
PDF |
Sep 20, 2004 |
Chris |
| √ |
Lecture 7 |
Database searching using FASTA and BLAST |
PDF |
Sep 23, 2004 |
Chris |
| √ |
Lecture 8 |
Statistical significance |
PDF |
Sep 27, 2004 |
Chris |
| √ |
Lecture 9 |
Multiple sequence alignment |
PPT |
Sep 30, 2004 |
John |
| √ |
Lecture 10 |
Editing MSAs |
PPT |
Oct 4, 2004 |
John |
| √ |
Lecture 11 |
Phylogenetic trees, distance-based |
PDF |
Oct 7, 2004 |
Chris |
| √ |
Lecture 12 |
Constructing trees using parsimony |
PDF |
Oct 12, 2004 |
Chris |
| √ |
Lecture 13 |
Weights, odds, profiles and logos |
PDF |
Oct 14, 2004 |
Chris |
| |
review session |
Oct 18, 2004 |
| |
-------MIDTERM------- |
Oct 21, 2004 |
| √ |
Lecture 16 |
Markov chains and hidden Markov models |
PDF |
Oct 25, 2004 |
Chris |
| √ |
Lecture 17 |
Pair HMMs, profile HMMs |
PDF |
Oct 28, 2004 |
Chris |
| √ |
Lecture 18 |
More profile HMMs |
PDF |
Nov 1, 2004 |
Chris |
| √ |
Lecture 19 |
Clustering sequences, HMMSTR (lec 18) |
PDF |
Nov 4, 2004 |
Chris |
| √ |
Lecture 20 |
Bayesian adaptive alignment,Motifs and footprints |
PDF |
Nov 8, 2004 |
Chris |
| √ |
Lecture 21 |
Single nucleotide polymorphisms |
PDF |
Nov 11, 2004 |
John |
| √ |
Lecture 22 |
RNA secondary structure |
PDF |
Nov 15, 2004 |
John |
| √ |
Lecture 23 |
PCR primer design |
PDF |
Nov 18, 2004 |
John |
| √ |
Lecture 24 |
Microrepeats, satelites and transposons |
PDF |
Nov 22, 2004 |
Chris |
| √ |
Lecture 25 |
Microarrays |
PDF |
Nov 29, 2004 |
John |
| √ |
Lecture 26 |
Gene finding, splicing |
PDF |
Dec 2, 2004 |
Chris |
| |
-------Student presentations------- |
Dec 6, 2004 |
| |
review session |
Dec 9, 2004 |
| |
-------Final Exam------- |
Dec 16, 2004 |