| Date | Description |
|---|---|
| January 3 |
Basics of molecular biology: proteins, DNA Hunter's primer Molecular Biology handout |
| January 5 | Basics of molecular biology: replication, gene expression |
| January 10 | Basics of molecular biology: gene structure, genome organization |
| January 12 |
Pairwise global alignment Lectures 3-5 from CSE 527 |
| January 17 | Pairwise local alignment, affine gap penalties |
| January 19 | Snow closure |
| January 24 |
BLAST Overview of the BLAST Algorithm Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990), "Basic local alignment search tool". Journal of Molecular Biology 215:403-410. |
| January 26 |
BLAST statistics; amino acid substitution matrices Section 6.5 from Ewens and Grant's book Stephen Altschul's primer |
| January 31 |
Multiple sequence alignment Lectures 6 from CSE 527 |
| February 2 |
Extremely Conserved Elements example of Theorem 2 |
| February 7 |
Progressive alignment; phylogeny construction Building phylogenies Overview of progressive alignment |
| February 9 |
Markov chains Markov Models |
| February 14 | Hidden Markov models; Viterbi algorithm |
| February 16 |
Profile HMMs Profile HMMs |
| February 21 |
Human microbiome Microbes and you |
| February 23 |
Human microbiome Genome assembly |
| February 28 | Forward-backward algorithm |
| March 1 |
Detecting recent positive selection Gusfield's notes |
| March 6 | Detecting recent positive selection |
| March 8 | TBD |