Syllabus
(version: August 30, 2002)
SEQUENCE ANALYSIS
Biochem 711
Fall Semester 2002, 2cr. Tues/Thurs, 9:55-10:45 a.m., 175 Biochemistry
Addition, 433 Babcock Drive.
Dr. Ann Palmenberg (ACP), Professor, Dept. of Biochemistry & Inst. for Molecular Virology,
R.M. Bock Laboratories, Rm 527B, 1525 Linden Drive; Ph: 262-7519; acpalmen@facstaff.wisc.edu
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When: |
What: |
Topics: (as of 8/30/02) |
Who: |
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Sept 03, Tues |
Class 1 |
Introduction, class resources, web site, grading requirements,
single letter codes |
ACP |
|
Sept 05, Thurs |
Class 2 |
RNA, DNA and Mutation Fixation I |
ACP |
|
Sept 10, Tues |
Class 3 |
RNA, DNA and Mutation Fixation II |
ACP |
|
Sept 12, Thurs |
Class 4 QUIZ
|
The Character of Amino Acids In-class quiz on single-letter
codes |
ACP |
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Sept 17, Tues |
Class 5 |
Orfs, Urfs and the Genetic Code Pick up book for 1st book
report |
ACP |
|
Sept 19, Thurs |
Class 6 |
2D Protein Structure Prediction |
ACP |
|
Sept 24, Tues |
Class 7 |
Structural Genomics |
GPhillips
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Sept 26, Thurs |
Class 8 |
Proteomics |
BFox
|
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Oct 01, Tues |
Class 9
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PAM, Blosum and Related Substitution Matrices |
ACP |
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Oct 03, Thurs |
Class 10 EXAM 1
|
In-class exam on material to date
|
EXAM 1 |
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Oct 08, Tues |
Class 11 |
Pairwise Comparison with DotPlots |
ACP |
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Oct 10, Thurs |
Class 12 |
Pairwise Comparisons with Optimal Alignments |
ACP |
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Oct 15, Tues |
Class 13 |
Profiles and Multiple Sequence Alignments |
ACP |
|
Oct 17, Thurs |
Class 14 BkRept 1 due |
Consensus Sequences 1st book report due. Exchange books |
ACP |
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Oct 22, Tues |
Class 15 |
Gene Finding using Hidden Markov Models (HMMs) |
SSmith |
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Oct 24, Thurs |
Class 16 |
Database Searching: FastA |
ACP |
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Oct 29, Tues |
Class 17 |
Database Searching: Blast |
ACP |
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Oct 31, Thurs |
Class 18 |
Phylogenetic Reconstruction I: Trees |
ACP |
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Nov 05, Tues |
Class 19 |
Phylogenetic Reconstruction II: Distance vs Parsimony
|
ACP |
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Nov 07, Thurs |
Class 20 EXAM 2 |
In-class exam on material since previous exam
|
EXAM 2 |
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Nov 12, Tues |
Class 21 |
Phylogenetic Reconstruction III: (tentative title) |
AWolf |
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Nov 14, Thurs |
Class 22 |
Sequencing Strategies |
GPlunkett |
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Nov 19, Tues |
Class 23 |
Sequence Databases |
GPlunkett |
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Nov 21, Thurs |
Class 24 |
Massively Parallel Methods for Analyzing Transcriptomes
& Proteosomes (aka: Gene Chips) |
MSussman |
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Nov 26, Tues |
Class 25 BkRept 2 due |
Optimal RNA Folding
2nd book report due. Return all books |
ACP |
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Nov 28, Thurs |
no class |
Thanksgiving
|
- |
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Dec 03, Tues |
Class 26 |
New Methods for Processing Chip Data (tentative title) |
BYandell |
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Dec 05, Thurs |
Class
27
|
Suboptimal
RNA Folding |
ACP |
|
Dec 10, Tues |
Class 28 |
DNA Profiling in Criminal
Cases |
AFriedman |
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Dec 12, Thurs |
Class 29 EXAM 3 |
In class exam on semester material
|
EXAM 3 |
Course Web Page(s) and Online Resources:
http://virology.wisc.edu/acp
Guest Speakers and Contacts for 2002
Dr. Jean-Yves Sgro, BNMC Genetics Computing Research Consultant, bnmc_res@gene.biotech.wisc.edu
Ms. Marchel Hill, Sr. Research Specialist, 511A BockLabs, mhill@biochem.wisc.edu
Ms. Rachel Groppo, Biochem Grad Student (TA), 527B BockLabs, rgroppo@biochem.wisc.edu
Dr. George Phillips, Professor, Dept. of Biochemistry, UW-Madison, phillips@biochem.wisc.edu
Dr. Brian Fox, Professor, Dept. of Biochemistry, UW-Madison, bgfox@biochem.wisc.edu
Dr. Michael Sussman, Professor, Dept. of Biochemistry, UW-Madison, msussman@facstaff.wisc.edu
Mr. Steve Smith, Nimblegen, Madison, WI, ssmith@nimblegen.com
Dr. Brian Yandell, Professor, Depts of Horticulture and Statistics, UW-Madison,
byandell@facstaff.wisc.edu
Dr. Alan Wolf, Director, Biology New Media Center, UW-Madison, ajwolf@doit.wisc.edu
Dr. Guy Plunket, Assoc. Scientist, Laboratory of Genetics, UW-Madison, guy@genome.wisc.edu
Dr. Alan Friedman, President, Helix Biotech, Milwaukee, WI, helix@execpc.com