TENTATIVE SCHEDULE FOR CPT S 580 Computational Genomics (Spring'09)
| Class | Day | Date | Topic |
Assignments* |
|
| Due | Posting | ||||
| 1 | Tue | 1/13 | Course Introduction, Computational biology & bioinformatics | ||
| 2 | Thu | Approximate matching, Global alignment | |||
| 3 | Tue | 1/20 | Local alignment | ||
| 4 | Thu | Affine gap penalty | Program 1 | ||
| 5 | Tue | 1/27 | Semi-global alignment | ||
| 6 | Thu | space-optimal alignment | HW1 | ||
| 7 | Tue | 2/3 | Hirschberg technique | ||
| 8 | Thu | k-band algorithm, Edit distance, Longest common subsequence problem | Program 1 | ||
| 9 | Tue | 2/10 | Exact Matching, Lookup tables, tries | ||
| 10 | Thu | PATRICIA tree, suffix tree, suffix array (definitions) | HW1 | ||
| 11 | Tue | 2/17 | Suffix links, Suffix array + LCP | HW2 | |
| 12 | Thu | Kasai algorithm | |||
| 13 | Tue | 2/24 | Suffix tree construction: McCrieght algorithm | ||
| 14 | Thu | Lowest common ancestor problem (Bender-Farach algo) | |||
| 15 | Tue | 3/3 | " | HW2 | |
| 16 | Thu | suffix tree applications | |||
| 17 | Tue | 3/10 | " | Program 2 | |
| 18 | Thu | Probabilistic modeling, Markov models, CpG islands | HW3 | ||
| -- | Tue | 3/17 | SPRING BREAK HOLIDAYS | ||
| -- | Thu | ||||
| 19 | Tue | 3/24 | Hidden Markov models (HMM) | ||
| 20 | Thu | Viterbi algorithm | |||
| 21 | Tue | 3/31 | Forward and backward algorithm | HW3 | |
| 22 | Thu | Baum-Welch | |||
| 23 | Tue | 4/7 | MIDTERM EXAM | ||
| 24 | Thu | Genome assembly algorithm | |||
| 25 | Tue | 4/14 | Phylogenetics | Program 2 | |
| 26 | Thu | " | |||
| 27 | Tue | 4/21 | " | ||
| 28 | Thu | Survey project presentations | |||
| 29 | Tue | 4/28 | Survey project presentations | ||
| 30 | Thu | Survey project presentations | |||
| -- | Tue | 5/5 | FINALS WEEK | ||
| -- | Thu | ||||
* Homework & program links will be activated on their posting dates.