Syllabus

Meeting Time/Location: Tuesday- Thursday 10:30-11:50 am HSB J-280.

Part One: Analyzing Whole Genomes.

Debbie Nickerson and Barbara Trask

T Oct. 2 Course Overview/Background Perspective. Trask.

Th Oct. 4 Defining Genomes. Trask.

T Oct. 9 UW Genome Center Tour, Fluke Hall. UWGC Staff.

Th Oct. 11 Overview of Genome Technologies. Nickerson.

T Oct. 16 Mapping/Sequencing Genomes I.

Th Oct. 18 Mapping/Sequencing Genomes II.

T Oct. 23 Genome Variation - Technologies and Applications

Th Oct. 25 Emerging Technologies and Applications.

Part Two: Analyzing Function by Protein Homology.

Jim Thomas

T Oct. 30 Introduction, overview of sequence alignment.

Dynamic programming and BLAST alignment methods.

Th Nov. 1 Web-based sequence databases. BLAST searching, Psi-BLAST.

T Nov. 6 Using Clustal for multiple alignment, pretty alignment figures.

Evolutionary trees and protein families.

Th Nov. 8 Protein domains. Correlating alignments and 3-D protein structures. Using structure viewers.

T Nov. 13 Sequence divergence, alignments, structure: case study of CaM

Kinase II, the CaM kinase family, and kinase superfamily.

Th Nov. 15 CaM Kinase II mutagenesis studies - structure/function.

Evolution as nature's mutagenesis study.

Part Three: Analyzing Function by Classical Genetic Approaches.

Celeste Berg