| Date | Description |
|---|---|
| January 8 |
Basics of molecular biology: proteins, DNA, replication Hunter's primer Molecular Biology handout |
| January 10 | Basics of molecular biology: gene expression and structure |
| January 15 |
Pairwise global alignment Lectures 3-5 from CSE 527 |
| January 17 | Pairwise local alignment, affine gap penalties |
| January 22 |
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 24 |
BLAST statistics; amino acid substitution matrices Section 6.5 from Ewens and Grant's book Stephen Altschul's primer |
| January 29 |
Multiple sequence alignment Lectures 6 from CSE 527 Overview of progressive alignment |
| January 31 |
UCSC Genome Browser, Extremely Conserved Elements example of Theorem 2 |
| February 5 |
Phylogeny construction Building phylogenies |
| February 7 |
Markov chains and classification Markov Models |
| February 12 | Hidden Markov models |
| February 14 |
Profile HMMs Profile HMMs |
| February 19 |
Motif discovery; statistical overrepresentation; MEME Prediction of sequence motifs |
| February 21 | Gibbs sampling; FootPrinter |
| February 26 |
MicroFootPrinter MEME and Gibbs demo |
| February 28 | Technical details of profile HMMs |
| March 5 |
Microbiomes Microbes and You |
| March 7 | More profile HMMs and microbiomes |
| March 12 |
Colonization of infant gut Infant gut microbiome |
| March 14 |
Other directions, Schnapsen Challenges in computational biology |