Syllabus  (version: Sept 15, 2004)

 

                                                              SEQUENCE ANALYSIS

                                                                        Biochem 711

Fall Semester 2004, 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@wisc.edu

 

When:

What:

Topics:

Who:

Sept 02, Thurs

Class 1

Introduction, class resources, web site, grading requirements, single letter codes

ACP

Sept 07, Tues

Class 2

RNA, DNA and Mutation Fixation I

ACP

Sept 09, Thurs

Class 3

RNA, DNA and Mutation Fixation II

ACP

Sept 14, Tues

Class 4

QUIZ

The Character of Amino Acids

In-class quiz on single-letter codes

ACP

Sept 16, Thurs

Class 5

Orfs, Urfs and the Genetic Code

Pick up book for 1st book report

ACP

Sept 21, Tues

Class 6

2D Protein Structure Prediction

ACP

Sept 23, Thurs

Class 7

Structural Genomics

G. Phillips

Sept 28, Tues

Class 8

PAM, Blosum and Related Substitution Matrices

ACP

Sept 30, Thurs

Class 9

Exam 1

In-class exam on material to date

  

 

Oct 05, Tues

Class 10

Pairwise Comparisons with Dot Plots

ACP

Oct 07, Thurs

Class 11

Pairwise Comparisons with Optimal Alignments

ACP

Oct 12, Tues

Class 12

Profiles and Multiple Sequence Alignments

ACP

Oct 14, Thurs

Class 13

 BkRpt 1 due

Consensus Sequences

1st book report due.  Exchange books

ACP

Oct 19, Tues

Class 14

Gene Finding with HMMs

S. Smith

Oct 21, Thurs

Class 15

Database Searching: FastA

ACP

Oct 26, Tues

Class 16

Database Searching: Blast

ACP

Oct 28, Thurs

Class 17

Phylogenetic Reconstruction I: Trees

ACP

Nov 02, Tues

Class 18

Phylogenetic Reconstruction II: Distance vs Parsimony

ACP

Nov 04, Thurs

Class 19

Exam 2

 

In-class exam on material to date

ACP

Nov 09, Tues

Class 20

Phylogenetic Reconstruction III: Selecting among Trees

A. Wolf

Nov 11, Thurs

Class 21

Databases and Chromosome Maps

ACP

Nov 16, Tues

Class 22

Sequencing Strategies and Data Analysis

N. Perna

Nov 18, Thurs

Class 23

Topic:  TBA

 

Nov 23, Tues

Class 24

BkRept 2 due

Proteomics

2nd book report due.  Return all books

B. Fox

Nov 25, Thurs

no class

Thanksgiving

 

Nov 30, Tues

Class 25

Optimal RNA Folding

ACP

Dec 02, Thurs

Class 26

Sub-Optimal RNA Folding

ACP

Dec 07, Tues

Class 27

Massively Parallel Methods for Analyzing Transcriptomes & Proteosomes (aka: Gene Chips)

M. Sussman 

Dec 09, Thurs

Class 28

Practical Approach to Molecular Modeling

J. Sgro

Dec 14, Tues

Class 29

EXAM 3

In class exam on semester material

ACP

 

 

 

Course Web Page(s) and Online Resources:    

 

            http://virology.wisc.edu/acp

 

Guest Speakers and Contacts for 2004

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

 

Mr. Fred Porter, Biochem Grad Student (TA), 527B BockLabs,  fporter@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. Alan Wolf, Director, Biology New Media Center, UW-Madison,  ajwolf@doit.wisc.edu

 

Dr. Nicole Perna, Asst Professor, Dept AH&BS, Biotechnology Center,  perna@ahabs.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