Date | Lecture Topic(s) | Due | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Fri 27 Sept 2013 | 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 30 Sept 2013 | Python tutorial | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 2 Oct 2013 | DNA sequencing (went over table
from
Wikipedia DNA
Sequencing—except SOLiD):
Discussed different error types for different sequencing methods. Also discussed paired-end and mate-pair library construction. Challenge: how is error rate measured for polymerases? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 4 Oct 2013 | What is a probability function? (domain=event space, range=[0,1], sums to 1). Stochastic model is computable probability function. Developed uniform probability for strings of given length. Challenge: extend to strings of any length. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 7 Oct 2013 | Discussed bugs in HW 1 (forgetting to include apostrophe in letters, wrong sort order). Also covered tips on various ways to split line into words, to specify sort order, and to do mutual exclusion of options. Covered stop character as one way to get stochastic model for all strings (gave terms "i.i.d." and "zero-order Markov"). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 9 Oct 2013 | Answered questions about FASTA/FASTQ assignment. Discussed ways to measure DNA polymerase accuracy (using lacZ reporter). Reviewed i.i.d. with stop character and got length distribution by marginalizing. Used Socratic dialog to develop factored length and i.i.d. model. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 11 Oct 2013 | Discussed fellowship applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 14 Oct 2013 | Discussed Python problems seen in 2nd homework. Covered a couple more Python idioms (including izip). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 16 Oct 2013 | Markov chains. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 18 Oct 2013 | coding cost, information gain, entropy, relative entropy. Counts to probabilities to log-P. pseudocounts. (MLE and MAP). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 21 Oct 2013 | Writing problems (research overview first, specific aims, topic sentences, avoid "this" as pronoun, old info->new info, comma splices, "however" is not conjunction, "would" used primarily for contrary-to-fact in tech writing). Questions about Markov chain assignment. How to sum probabilities in log-prob representation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 23 Oct 2013 | Answered questions on Markov chain assignment. First part of "better than chance" lecture on null models. P-values and E-values. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 25 Oct 2013 | Second part of "better than chance" | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 28 Oct 2013 | Finished "better than chance" introduced substitution matrices as log P(aligned)/P(independent) and described how BLOSUM matrices are created. Talked little about PAM matrices. Lecture may have been rough due to fatigue. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 30 Oct 2013 | Python problems and idioms that came up in Markov-model assignment. A lot of time spent on what documentation needs to contain and why. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 1 Nov 2013 | Presentation by Ann Hubble in Science Library. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 4 Nov 2013 | Feedback on programming for palindrome assignment. Started on alignment, covering gapless alignment. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 6 Nov 2013 | Guest lecture by Dent Earl. Google doc presentation | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 8 Nov 2013 | Substitution matrices, PAM, BLOSUM. Gapless alignment, dynamic programming, traceback | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 11 Nov 2013 | Veteran's Day (no class) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 13 Nov 2013 | Feedback on homework. Alignment with arbitrary gap costs. Memoized vs dynamic programming. BLAST and prefiltering. Dot plots. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 15 Nov 2013 | Arbitrary gap costs. Global alignment and local, recurrence relations, matrices. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 18 Nov 2013 | Linear gap costs. Global and local. Traceback. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 20 Nov 2013 | Building locked. No class. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 22 Nov 2013 | Affine gap alignment (global and local, traceback). A2M format. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 25 Nov 2013 | Feedback on paper, some further discussion of affine-gap alignment traceback. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 27 Nov 2013 | Intro to HMMs. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 29 Nov 2013 | Thanksgiving (no class) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mon 2 Dec 2013 | HMM review (forward and Viterbi), local alignment by changing HMM, building HMM from multiple sequence alignment (thinning, Henikoff sequence weighting, brief mention of Dirichlet mixtures), EM and Lagrangian multipliers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Wed 4 Dec 2013 | EM & Lagrangian multiplier review, Baum-Welch training, expected value of other functions of state, HMM for base-caller on nanopores | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Fri 6 Dec 2013 | Overview of read types (including paired-end and mate pair), genome assembly, overlap-consensus graph, de Bruijn graph, k-mer cleaning, coverage needed | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Thurs 12 Dec 2013 | 8a.m.–11a.m. exam slot, not used |
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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