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BME110: Computational Biology Tools

Winter 2004
MWF 11:00-12:20
Baskin Engineering 156

Carol Rohl
rohl @ ucsc.edu
Office Hours: Th 3-5pm
220 Sinsheimer
Todd Lowe
lowe @ soe.ucsc.edu
Office Hours: T,F 2-3pm
227 Sinsheimer

Corey Powell
cpowell @ soe.ucsc.edu
Office Hours: to be announced

Catalog Description:
Hands-on laboratory geared to teach basic tools used in computational biology (motif searching, primer selection, sequence comparison, multiple sequence alignment, genefinders, phylogenetics analysis, X-ray crystallography software). Web- and Unix-based tools/databases are used. Open to all science students; no prior Unix experience required.

A goal in this course is for students to set up their own bioinformatics environment on the operating system with which they are most confortable. We highly encourage students to bring a laptop to class. If possible, we will conduct lab sessions and lectures concurrently, making use of the networking capabilities BE156. If you do not have access to a laptop computer that you can use for this class, please contact the instructors as soon as possible.

Required Texts
Bioinformatics for Dummies
Jean-Michel Claverie & Cedric Notredame
Wiley Publishing, 2003
online resources

Developing Bioinformatics Computer Skills
Cynthia Gibas & Per Jambeck
O'Reilley & Associates, 2001
Additional Resources
Introduction to Bioinformatics
Arthur Lesk
Wiley Publishing, 2003
Bioinformatics and Functional Genomics
Jonathan Pevsner
John Wiley & Sons, 2003

Problem Sets: 80%
Final Exam: 20%

Course Outline: (syllabus)
Week 1: Using Bioinformatics Resources

Week 2: Single Sequence Analysis Week 3: Pairwise Sequence Comparison Week 4: Dynamic Programming, PSI-BLAST

Week 5: Multiple Sequence Alignment; Remote Homology Detection

Week 6: Orthologs, Paralogs and Trees Week 7: Protein Structures Week 8: Building Structural Models Week 9: Genome Analysis; Specialized Gene Finders Week 10: Advanced Topics