| Date | Lecture Topic(s) | Due |
|---|---|---|
| Fri 24 Sept | administrivia | |
| Mon 27 Sept | fundamental dogma, DNA, RNA | |
| Wed 29 Sept | protein backbones: torsion angles, CORN heuristic for chirality, parallel & antiparallel strands, type 1 and type 2 hairpin turns, helices, Z twist, sidechains: GLY and PRO, cis peptides | |
| Fri 1 Oct | amino-acid side chains: codes, structures, and properties | |
| Mon 4 Oct | Phoenix Eagleshadow (fellowships); Bayes Rule, importance of good null model, 0-order Markov chain, simple length model, intro to 1st-order Markov chain | |
| Wed 6 Oct | 1st-order Markov models, stop characters for finite strings, training Markov models, maximum-likelihood estimate, pseudocounts for Markov models, train/test and cross-validation, need for redundancy reduction. | perl 1 (noon) |
| Fri 8 Oct | train/cross-train/test, training first-order Markov, maximum likelihood estimate, intro to pseudocounts, use of log-probability, adding probabilities in log-prob representation (efficient computation of log(exp(x)+exp(y)) ), arbitrary scoring systems (Gaussian and Gumbel distributions mentioned). | |
| Mon 11 Oct | Gaussian and Gumbel distributions (with formulas), P_1-value, P_n-value, E-value, entropy, relative entropy | |
| Wed 13 Oct | relative entropy, mutual information, using mutual information to predict base or residue interaction, small sample problems with contingency tables, random scrambling, E-values for mutual information, thinning multiple alignments to remove subfamily signal that "contaminates" residue-interaction signal. | Darling models (in-class) |
| Fri 15 Oct | sequence logos, measures of conservation, rasmol for viewing protein structures | |
| Mon 18 Oct | true positives/false positives ..., ROC plots, substitution matrices, socring gapless alignments. | |
| Wed 20 Oct | scoring with linear, affine, and abitrary gap costs, alignment graph, linear gap cost recursive function. | Fellowship application (noon) |
| Fri 22 Oct | dynamic programming (global, linear gap cost); computing score, low space score computation, backtrace | |
| Mon 25 Oct | Backtrace algorithm in detail for global linear gap cost. Parallel computation of score on Kestrel processor (diagonal at-a-time computation), local alignment with linear gap cost. | |
| Wed 27 Oct | global alignment with affine gap cost, deriving the recurrence and initial conditions, need for keeping track of state as well as row and column in backtrace | perl 2 (noon) |
| Fri 29 Oct | local alignment with affine gap cost (including review of global for large fraction of class that missed Wed), global alignment with arbitary gap costs | |
| Mon 1 Nov | Katherine Soehner and Christy Hightower (Science Library) | |
| Wed 3 Nov | Hidden Markov models: generating sequences and the forward algorithm | perl 3 (noon) |
| Fri 5 Nov | Viterbi and backward algorithm | |
| Mon 8 Nov | Baum-Welch training of HMMs, Profile HMMs | |
| Wed 10 Nov | Local structure and neural nets | |
| Fri 12 Nov | Training neural nets | |
| Mon 15 Nov | Speck's low-memory alignment traceback; Dirichlet densities | |
| Wed 17 Nov | mixtures of Dirichlets | perl 4 (noon) |
| Fri 19 Nov | linear-memory alignment; sequence weighting (motivation, Henkoffs' method, absolutw weighting by target entropy) | |
| Mon 22 Nov | multiple alignment: progressive alignment and iterative refinement: MUSCLE | |
| Wed 24 Nov | putting it all together: the SAM-T2K method for protein structure prediction | web and literature search (noon) |
| Fri 26 Nov | NO CLASS | |
| Mon 29 Nov | ||
| Wed 1 Dec | perl 5 noon | |
| Fri 3 Dec | Guest lecture: M. Elizabeth Corey evolutionary trees | |
| Mon 6 Dec 12--3 | exam period (NOT USED) |
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| BME 100 home page | Karplus's lab page | UCSC Bioinformatics research |
Questions about page content should be directed to
Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250