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| SoE home |
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| Kevin Karplus's home page |
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| Biomolecular Engineering Department |
The lecture schedule reflects the material actually delivered. To get an idea what is coming up, see Fall 2013 schedule.
| Date | Lecture Topic(s) | Due |
|---|---|---|
| Fri 3 Oct 2014 | administrivia, texts,
assignments, structure of course. Fundamental dogma and
sequencing as a major source of bioinformatic data. Error rates of information copying (polymerases): DNA->DNA: Taq 1/125,000; Pfu 1/2,300,000; mitochondrial pol gamma ; 1/300,000-1/500,000; pol eta 1/18-1/38 RNA->DNA: HIV 1/1700-/8000; SIV 1/19,000; Accuscript RT 1/62,000 RNA->RNA: flu 1/10,000; Qbeta 1/3,000. Ribosome: Ecoli 1/3000; generally 1/2000-1/20,000. | intake survey |
| Mon 2014 Oct 6 | Unix permissions, stdin, Python for loop and yield with examples of line-at-a-time input, multiple returns as a tuple, a little on string member functions and immutability of strings, a little on docstring vs. comment | intake survey |
| Wed 2014 Oct 8 | DNA sequencing technologies, with notes from https://en.wikipedia.org/wiki/DNA_sequencing#table | |
| Fri 2014 Oct 10 | what is a probability function? a stochastic model? Developing i.i.d. model for strings of fixed length. | Python scaffold |
| Mon 2014 Oct 13 | feedback on 1st Python program. | |
| Wed 2014 Oct 15 | i.i.d model for arbitary length strings (separate length model and stop character model producing exponential distribution). Markov chains. | |
| Fri 2014 Oct 17 | Fellowships, start model uses | fasta/fastq parsing |
| Mon 2014 Oct 20 | Programming hints: problem decomposition, importance of specifying clean interafaces, examples from endtrim homework | |
| Wed 2014 Oct 22 | uses of models (generation, classification, search). Need for "how well do model and data fit". coding cost, log-likelihood ratio, prior and posterior ratios. | |
| Fri 2014 Oct 24 | review: coding cost, info gain=log-likelihood ratio. expected value, entropy, relative entropy, optimize log likelihood (MLE), Lagrangian multipliers to get MLE for i.i.d. model using {A,C,G,T}. Handwaving approach to pseudocounts as update to Dirichlet distribution over all models. Soft priors vs. stiff priors. Add-one prior. | fellowship |
| Mon 2014 Oct 27 | Writing feedback: topic
sentences, old info→new info, avoid generic
statements, Answered questions about Markov chain assignment. | |
| Wed 2014 Oct 29 | questions about Markov chain assignment, Better than chance talk through example 1, model 2. | |
| Fri 2014 Oct 31 | train/cross-train/test and n-fold cross-validation (as answer to question, not planned), Better than chance finished example 1 | Markov chains |
| Mon 2014 Nov 3 | some feedback on Markov chain homework, library session | |
| Wed 2014 Nov 5 | model for palindromes | |
| Fri 2014 Nov 7 | analyzing two approaches to computing expected count for odd palindromes, for CATSATG in H. influenzae; One more slide of Better than chance | palindromes |
| Mon 2014 Nov 10 | Substitution matrices and gapless alignment | |
| Wed 2014 Nov 12 | Global arbitrary-gap alignment | |
| Fri 2014 Nov 14 | Global linear-gap alignment | protein paper |
| Mon 2014 Nov 17 | feedback on protein paper, questions about null models, local linear-gap alignment. | |
| Wed 2014 Nov 19 | questions about null model assignment, explanation of A2M format, local affine-gap alignment | |
| Fri 2014 Nov 21 | class canceled—students attend lab rotation talks | null models |
| Mon 2014 Nov 24 | worked out example of local affine-gap alignment, partially worked out example of global affine-gap alignment | |
| Wed 2014 Nov 26 | questions about alignment. intro to HMMs through forward algorithm | |
| Fri 2014 Nov 28 | Thanksgiving, no class | |
| Mon 2014 Dec 1 | feedback on null models, log(e^x+e^y) algorithm, profile HMMs | |
| Wed 2014 Dec 3 | questions about degenerate-codon assignment, messed up intro to EM, review of forward algorithm, need for backward algorithm | alignment |
| Fri 2014 Dec 5 | Lagrangian multipliers to optimize P(x|theta) with constraints on emissions and transitions, derivation of backwards algorithm, Baum-Welch updates for emissions and transitions (no silent states) | |
| Mon 2014 Dec 8 | protein stucture prediction (iterated search, sequence logos, neural nets for secondary structure) | |
| Wed 2014 Dec 10 | more on structure prediction, various protein local-structure alphabets, multi-track HMMs | |
| Fri 2014 Dec 12 | quick overview of tree-building: phylogenetic an other types of hierarchical clustering, rooted vs.unrooted, outgroups, parsimony, maximum likelihood, distance-based mthods, simple distance function -log(1-4/3 DNA change), UPGMA, progressive alignments, neighbor-joining | |
| Wed 2014 Dec 17, 4–7 p.m. | final exam slot, no class | degenerate codons (and all REDOs) |
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| BME 205 home 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
318 Physical Sciences Building
