CISC-471: Computational Biology(also known as: CMPE-471) |
(Fall 2018) |
Monday | 8:30-10:00 | Kingston Hall RM 208 |
Thursday | 10:00-11:30 | Kingston Hall RM 208 |
Monday | Thursday | |
Week 1 Introduction. |
September 3 First Class is on Thursday, Sept. 6. |
September 6 Introduction/ Finding most frequent k-mers Watch this video: The Search for Hidden Messages in the Replication Origin (Part 1). In particular near the 10 minute mark he discusses different approaches to solve the most frequent k-mer problem. Homework 1. |
Week 2 Introduction. |
September 10 Finding most frequent k-mers, continued. Review of Big-Ο, Big-Ω, Big-Θ Making Change See Section 2.3 of the text. |
September 13 Solutions to Homework #1 |
Week 3 Exhaustive Search. (Chapter 4) |
September 17 Restriction Mapping. See section 4.1-4.3 of the text. Homework 2. Be prepared to share your solutions with classmates in class on Thursday September 20 |
September 20 Solutions to Homework #2 Motif finding. See section 4.4-4.9 of the text. Homework 3. Be prepared to share your solutions with classmates in class on Thursday September 27. |
Week 4 Greedy Algorithms (Chapter 5) |
September 24 Median, motif, branch and bound, sorting by reversals. |
September 27 Solutions to Homework #3 Sorting by reversals see Chapter 5. Homework 4. Be prepared to share your solutions with classmates in class on Thursday Oct. 4. |
Week 5 Dynamic Programming Algorithms (Chapter 6) |
October 1 |
October 4 Solutions to Homework #4 |
Week 6 |
October 8 THANKSGIVING. No class. |
October 11 Quiz #1 base on homework 1, 2, 3, and 4 |
Week 7 Dynamic Programming Algorithms (Chapter 6) |
October 15 Homework 5. Due October 18. |
October 18 Be prepared to share your homework #5 solutions in class. |
Week 8 Dynamic Programming Sequence Alignment (Chapter 6) |
October 22 Global Alignmet, Local Alignment. Homework 6. Due November 1. |
October 25 FALL BREAK. No class. |
Week 9 Dynamic Programming Sequence Alignment (Chapter 6) |
October 29 |
November 1 Be prepared to share your homework #6 solutions in class. Space efficient sequence alignment. Homework 7. Due November 7. |
Week 10 Graph Algorithms. |
November 5 Sequencing by Hybridization, Euler tours |
November 8 Euler tours Homework 8. Due November 15. |
Week 11 |
November 12 Class moved to Jeffry 102 |
November 15 Class moved to Jeffry 422. |
Week 12 |
November 19 |
November 22 Quiz #2 Based on homework 5,6,7,8. |
Week 13 |
November 26 |
November 29 |
Numeric Range | Letter Grade | GPA |
90-100 | A+ | 4.3 |
85-89 | A | 4.0 |
80-84 | A- | 3.7 |
77-79 | B+ | 3.3 |
73-76 | B | 3.0 |
70-72 | B- | 2.7 |
67-69 | C+ | 2.3 |
63-66 | C | 2.0 |
60-62 | C- | 1.7 |
57-59 | D+ | 1.3 |
53-56 | D | 1.0 |
50-52 | D- | 0.7 |
0-49 | F | 0 |