CISC-471: Computational Biology(also known as: CMPE-471) |
(Winter 2015) |
Monday | 12:30-13:30 | Goodwin 521 |
Wednesday | 11:30-12:30 | Goodwin 521 |
Thursday | 13:30-14:30 | Goodwin 521 |
Monday | 2:30-4:30 | GOODWIN RM248 |
Monday | Wednesday | Thursday | |
Week 1 Introduction. |
January 5 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. |
January 7 Finding most frequent k-mers, continued. Review of Big-Ο, Big-Ω, Big-Θ |
January 8 Making Change See Section 2.3 of the text. |
Week 2 Exhaustive Search. (Chapter 4) |
January 12 Be prepared to share your homework solutions in class. |
January 14 Restriction Mapping. See section 4.1-4.3 of the text. |
January 15 Restriction Mapping. See section 4.1-4.3 of the text. |
Week 3 Exhaustive Search. (Chapter 4) Greedy Algorithms (Chapter 5) |
January 19 Be prepared to share your homework #2 solutions in class. Stef presented solutions in class today. I have appointed Jacob and Curtis to be presenters next week. If you want to be arrange presenting ahead of time send me an email message, or talk to me after class. |
January 21 Motif finding. See section 4.4-4.9 of the text. |
January 22 Genome Rearrangements See section 5.1-5.3 |
Week 4 Greedy Algorithms (Chapter 5) and Dynamic Programming Algorithms (Chapter 6) |
January 26 Be prepared to share your homework #3 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. |
January 28 Genome Rearrangements See section 5.4-5.5 |
January 29 Dynamic programming algorithms, sequence alignment Chapter 6 sections 6.1-6.2 |
Week 5 Dynamic Programming Algorithms (Chapter 6) |
February 2 Quiz #1. I will test your knowledge of material that is related to Homeworks 1 -3. The Quiz will be held in Goodwin Hall Room 254. |
February 4 Solutions to Quiz #1. Edit distance and sequence alignment |
February 5 Edit distance and and sequence alignment, Chapter 6 sections 6.4-6.5 |
Week 6 Dynamic Programming Algorithms (Chapter 6) |
February 9 Be prepared to share your homework #4 a.k.a. homework #5 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. |
February 11 Global sequence alignment and scoring alignments sections 6.6 and 6.7. |
February 12 Local sequence alignment section 6.8 |
Reading week |
February 16 |
February 18 |
February 19 |
Week 7 Dynamic Programming Sequence Alignment (Chapter 6) |
February 23 Be prepared to share your homework #6 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. |
February 25 Alignment with Gap Penalties. I have prepared an example that illustrates an algorithm that performs global alignment with affine gap penalties. |
February 26 Multiple Alignment |
Week 8 Divide and Conquer (Space efficient Sequence Alignment) |
March 2 Note that homework is due on Wednesday this week. Space efficient sequence alignment. |
March 4 Be prepared to share your homework #7 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. |
March 5 DNA sequencing, Shortest Superstring Problem, Traveling Salesman Problem. |
Week 9 Graph Algorithms |
March 9 Quiz #2. I will test your knowledge of material that is related to Homeworks 4 - 7. The Quiz will be held in Goodwin Hall Room 254. |
March 11 Presentation on NP-complete problems. Sequencing by Hybridization, Euler tours |
March 12 Euler tours, Interval graphs |
Week 10 Combinatorial Pattern Matching Suffix Tree |
March 16 Solutions to Quiz 2. Exact pattern matching, Trie |
March 18 Suffix Tree |
March 19 Be prepared to share your homework #8 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. |
Week 11 Gene Database Search |
March 23 Quiz #3. |
March 25 Approximate pattern matching using filtration, Gene Database Search, the BLAST algorithm. |
March 26 The BLAST algorithm, k-means clustering. |
Week 12 Review |
March 30 Solutions to Quiz #3 Review. |
April 1 Class is cancelled to allow participation in the School of Computing "Creative Computing Showcase. |
April 2 Be prepared to share your homework #9 solutions in class. If you want to arrange presenting ahead of time send me an email message, or talk to me after class. Final review. The Final will be based on homework 1-9. |