| No. | Date | Topic | Reading before class | Handouts | Assignments | |
|---|---|---|---|---|---|---|
| 1 | Jan. 15 | Introduction & What is interesting in a sequence? | Course description | |||
| 2 | Jan. 17 | Resources: Entrez | ||||
| 3 | Jan. 22 | Resources: Entrez and other databases | Assignment 1 (doc, pdf) Notes |
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| 4 | Jan. 24 | Sequence Similarity & Sequence Function | ||||
| 5 | Jan. 29 | Basic Probability and Statistics | Basic Probability | Assignment 1 due Assignment 2 (doc, pdf) |
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| 6 | Jan. 31 | Poisson, Binomial and Bayesian | Binomial and Poisson | |||
| 7 | Feb. 5 | Poisson, Binomial and Bayesian | Shotgun Sequencing Bayesian Statistics |
Assignment 2 due Assignment 3 (doc, pdf) |
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| 8 | Feb. 7 | Local Sequence Similarity | ||||
| 9 | Feb. 12 | Local Sequence Similarity: Probabilities & Scores | Assignment 3 due | |||
| 10 | Feb. 14 | Sequence Similarity & Sequence Function | Sequence Similarity | Assignment 4 (doc, pdf) | ||
| 11 | Feb. 19 | Sequence Similarity & Sequence Function | ||||
| 12 | Feb. 21 | Conserved Domains, Psi-BLAST & Profiles | Assignment 4 due Assignment 5 (doc, pdf) & pep1.txt |
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| 13 | Feb. 26 | Global Alignment and Multiple Sequence Alignment | Global Alignment | |||
| 14 | Feb. 28 | Multiple Alignment and Loose Ends | Assignment 5 due Assignment 6 (doc, pdf) & dna1.txt |
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| 15 | Mar. 4 | NMPDR and The SEED--Dr. Claudia Reich | ||||
| 16 | Mar. 6 | More on The SEED | Assignment 6 due | |||
| 17 | Mar. 11 | Horizontal Gene Transfer | ||||
| 18 | Mar. 13 | Codon Usage | ||||
| Mar. 18 | Spring Break | Play hard | ||||
| Mar. 20 | Spring Break | Play hard | ||||
| 19 | Mar. 25 | Phylogeny: Introduction & Maximum Parsimony | Phylogenetic Analysis | |||
| 20 | Mar. 27 | Phylogeny: Models, Distances & Maximum Likelihood | Assignment 7 (doc, pdf) & Addendum |
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| 21 | Apr. 1 | Phylogeny: Maximum Likelihood 2 & Bayesian | ||||
| 22 | Apr. 3 | Phylogeny: Errors & Uncertainties | Assignment 8 (doc, pdf) & Addendum |
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| 23 | Apr. 8 | Discussion of assignments | Assignment 7 due | |||
| 24 | Apr. 10 | More on phylogeny | Assignment 8 due Assignment 9 (doc, pdf) |
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| 25 | Apr. 15 | More on phylogeny | Assignment 10 (doc, pdf) & Addendum |
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| 26 | Apr. 17 | Subsystems and Consistency in Annotations | Assignment 9 due Assignment 11 (doc, pdf) & pep11.txt |
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| 27 | Apr. 22 | No Class | ||||
| 28 | Apr. 24 | Assignment 10 due Assignment 11 due Assignment 12 (doc, pdf) & Addendum |
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| 29 | Apr. 29 | Protein Thermal Adaptation (and the history of life) | Assignment 13 (doc, pdf) & Addendum |
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| May 2 | Final Examination Date (but no final) | Assignment 12 due (ways to turn it in) |
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| May 6 | Assignment 13 due (ways to turn it in) |