Syllabus  (version: Sept 1, 2006)

                                                              SEQUENCE ANALYSIS

                                                                        Biochem 711

 

Fall Semester 2006, 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 05, Tues

Class 1

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

ACP

Sept 07, Thurs

Class 2

RNA, DNA and Mutation Fixation I

ACP

Sept 12, Tues

Class 3

RNA, DNA and Mutation Fixation II

ACP

Sept 14, Thurs

Class 4

Quiz

The Character of Amino Acids

In-class quiz on single-letter codes

ACP

Sept 19, Tues

Class 5

Orfs, Urfs and the Genetic Code

Pick up book for 1st book report

ACP

Sept 21, Thurs

Class 6

2D Protein Structure Prediction

ACP

Sept 26, Tues

Class 7

PAM, Blosum and Related Substitution Matrices

ACP

Sept 28, Thurs

Class 8

Structural Genomics

G. Phillips

Oct 03, Tues

Class 9

Exam 1

In-class exam on material to date

  

 

Oct 05, Thurs

Class 10

Pairwise Comparisons with Dot Plots

ACP

Oct 10, Tues

Class 11

Pairwise Comparisons with Optimal Alignments

ACP

Oct 12, Thurs

Class 12

Profiles and Multiple Sequence Alignments

ACP

Oct 17, Tues

Class 13

 BkRpt 1 due

Consensus Sequences & Clustal

1st book report due.  Exchange books

ACP

Oct 19, Thurs

Class 14

Gene Finding with HMMs

S. Smith

Oct 24, Tues

Class 15

Database Searching: FastA

ACP

Oct 26, Thurs

Class 16

Database Searching: Blast

ACP

Oct 31, Tues

Class 17

Gene Chip Methods

M. Sussman 

Nov 02, Thurs

Class 18

Bioinformatics of Chip Datasets

J. Sgro

Nov 07, Tues

Class 19

Exam 2

In-class exam on material to date

 

Nov 09, Thurs

Class 20

Sequencing Strategies and Data Analysis

J. Glasner Tentative date/title

Nov 14, Tues

Class 21

Databases and Chromosome Maps

ACP

Nov 16, Thurs

Class 22

Phylogenetic Reconstruction I: Trees

ACP

 

 

 

 

Nov 21, Tues

Class 23

Phylogenetic Reconstruction II: Distance vs Parsimony

ACP

Nov 23, Thurs

no class

Thanksgiving

 

Nov 28, Tues

Class 24

BkRept 2 due

Phylogenetic Reconstruction III: Selecting among Trees

2nd book report due.  Return all books

(D. Baum)

tentative speaker

Nov 30, Thurs

Class 25

Proteomics

B. Fox

Dec 05, Tues

Class 26

Optimal RNA Folding

ACP

Dec 07, Thurs

Class 27

Sub-Optimal RNA Folding

ACP

Dec 12, Tues

Class 28

Topic:  TBA

 

Dec 14, Thurs

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 2006:

 

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

 

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

 

Dr Jeremy Glasner, Asst Scientist, UW Genome Center, UW-Madison, jeremy@genome.wisc.edu

 

Dr. Alan Wolf, Director, Biology New Media Center, UW-Madison,  ajwolf@doit.wisc.edu

 

Dr. David Baum, Professor, Botany Dept, UW-Madison, dbaum@wisc.edu

 

Dr. Brian Fox, Professor, Dept. of Biochemistry, UW-Madison,  bgfox@biochem.wisc.edu

 

Mr. Steve Smith, Nimblegen, Madison, WI,  ssmith@nimblegen.com