Tentative Schedule for CPT S 471/571 Computational Genomics (Spring'21)
The course will be organized into four major parts: i) Approximate string matching, ii) Exact string matching, iii) Probabilistic modeling, and iv) Advanced applications.
The topics mentioned provide a rough week-by-week schedule. It is subject to change as the semester progresses.Please also look out for instructor travel dates or university holidays as the semester progresses.
| Week | Day | Date | Topic |
| 1 | M |
1/18 | MLK Day - University holiday |
| |
W | First day of class: Course introduction, Introduction to computational biology, Bio-primer | |
| F | |||
| 2 |
M |
1/25 | Approximate
matching, Sequence alignment |
| W |
|
Global alignment , Local alignment, semi-global alignment | |
| F | |||
| 3 |
M |
2/1 | Affine gap penalty, Space-optimal
alignments |
| W |
|||
| F | |||
| 4 |
M | 2/8 | k-band algorithm, edit distance, LCS |
| W |
|||
| F | |||
| 5 |
M | 2/15 |
No Class (President's day) |
| W |
|
Exact Matching, Lookup table, tries | |
| F | |||
| 6 |
M | 2/22 | Suffix Trees and Suffix arrays: definitions and applications |
| W |
|||
| F | |||
| 7 |
M | 3/1 |
Suffix Tree and Suffix array - definitions
and applications |
| W |
|||
| F | |||
| 8 |
M | 3/8 | McCreight's algorithm, suffix links |
| W |
|
|
|
| F | |||
| 9 |
M | 3/15 | Suffix
tree construction algorithm and project description |
| W |
No Class (university break) | ||
| F | |||
| 10 |
M |
3/22 |
|
| W |
|
||
| F | |||
| 11 |
M | 3/29 | More suffix tree applications, LCA
computations |
| W |
|
||
| F | |||
| 12 |
M | 4/5 | Genome assembly and read mapping |
| W |
Genome graphs and assembly methods | ||
| F | |||
| 13 |
M | 4/12 |
Probabilistic modeling, Markov chains, CpG islands, HMMs |
| W |
|||
| F | |||
| 14 |
M | 4/19 | |
| W |
|
||
| F | Test Review |
||
| 15 |
M | 4/26 | Test Review; Survey project help |
| W |
|||
| F | Take Home Final Exam - posted on Blackboard | ||
| 16 | 5/3 | FINALS
WEEK:
For All Students: For CptS 571 students only: |
|
| |
|||
+ Denotes days when instructor will be on travel. Alternative arrangements for those classes will be communicated to the students as those days approach.