| No. | Date | Topic | Reading before class | Handouts | Assignments |
|---|---|---|---|---|---|
| 1 | Jan. 20 | Introduction & What can we learn from a sequence? | Course description | ||
| 2 | Jan. 22 | Resources: Entrez | PubMed summary | ||
| 3 | Jan. 27 | Resources: Entrez and other databases | Assignment 1 (PDF, doc) | ||
| 4 | Jan. 29 | Sequence Similarity & Sequence Function | |||
| 5 | Feb. 3 | Basic Probability and Statistics | Basic Probability | Assignment 1 due Assignment 2 (PDF, doc) |
|
| 6 | Feb. 5 | Binomial, Poisson and Bayesian | Binomial and Poisson | ||
| 7 | Feb. 10 | Binomial, Poisson and Bayesian | Bayesian Statistics | Assignment 2 due | |
| 8 | Feb. 12 | Local Sequence Similarity | Sequence Similarity | Assignment 3 (PDF, doc) | |
| 9 | Feb. 17 | Local Sequence Similarity: Probabilities & Scores | |||
| 10 | Feb. 19 | Sequence Similarity & Sequence Function | Assignment 3 due Assignment 4 (PDF, doc) |
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| 11 | Feb. 24 | Sequence Similarity & Sequence Function | |||
| 12 | Feb. 26 | Conserved Domains, Psi-BLAST & Profiles | Assignment 1 key(PDF) Assignment 2 key(PDF) |
Assignment 4 due | |
| 13 | Mar. 3 | Global Alignment and Multiple Sequence Alignment | Global Alignment | Assignment 5 (PDF, doc, pep1.txt) | |
| 14 | Mar. 5 | Multiple Alignment and Loose Ends | |||
| 15 | Mar. 10 | → Horizontal Gene Transfer ← | Assignment 5 due | ||
| 16 | Mar. 12 | NMPDR and The SEED — Dr. Claudia Reich | |||
| 17 | Mar. 17 | More on The SEED | Assignment 6 (revision) (PDF, doc, dna1.txt) | ||
| 18 | Mar. 19 | Codon Usage | |||
| Mar. 24 | Spring Break | Play hard | |||
| Mar. 26 | Spring Break | Play hard | |||
| 19 | Mar. 31 | Phylogeny: Introduction & Maximum Parsimony | Phylogenetic Inference | ||
| 20 | Apr. 2 | Phylogeny: Models, Distances & Maximum Likelihood | Assignment 3 key(PDF) | Assignment 7 (PDF, doc) | |
| 21 | Apr. 7 | Phylogeny: Maximum Likelihood 2 & Bayesian | |||
| 22 | Apr. 9 | Phylogeny: Errors & Uncertainties | Assignment 7 due Assignment 8 (PDF, doc) |
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| 23 | Apr. 14 | Phylogeny: Errors & Uncertainties | |||
| 24 | Apr. 16 | Thermal Adaptation | |||
| 25 | Apr. 21 | Subsystems and Consistency in Annotations | Assignment 8 due | ||
| 26 | Apr. 23 | Subsystems and Consistency in Annotations | Assignment 9 (PDF, doc, GlnRS.txt) | ||
| 27 | Apr. 28 | RNA Structure | Assignment 4 key(PDF) Assignment 5 key(PDF) |
Assignment 10 (PDF, doc, pep10a, dna10a) | |
| 28 | Apr. 30 | Assignment 6 key(PDF) Assignment 7 key(PDF) |
Assignment 9 due | ||
| 29 | May 5 | Assignment 8 key(PDF) Assignment 9 key(PDF) Assignment 10 key(PDF) |
Assignment 10 due | ||
| May 13 | Final Examination Date (but no final) |