BME110: Computational Biology Tools

Spring 2005
Tue/Thur 2-3:45pm
Baskin Engineering 156

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Todd Lowe
Email: lowe @
Office: 227 Sinsheimer
Phone: 459-1511
Office Hours:
    Tues 1-2pm, Thurs 4-5pm

Elizabeth Corey
Email: ecorey
Office: 309B Baskin Engineering
Office Hours: Thurs 1-2pm


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-based tools and databases are used. Open to all science students, with basic biochemistry or permission of the instructor as a  prerequsite.

Teaching Assistant:
David Bernick (dbernick
Hours: 12-2pm Tues, 8-10am Thurs, Baskin Eng. 308

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

Additional Resources
Introduction to Bioinformatics
Arthur Lesk
Wiley Publishing, 2003
Bioinformatics and Functional Genomics
Jonathan Pevsner
John Wiley & Sons, 2003

Problem Sets: 50%
Midterm: 15%
Final Exam: 30%

Course Outline: (See class calendar for any changes to original topic schedule)

Week 1: Using Bioinformatics Resources

Week 2: Single Sequence Analysis
Week 3: Pairwise Sequence Comparison, BLAST
Week 4: Sensitive Protein Searching

Week 5: Multiple Sequence Alignment & Phylogenetics

Week 6: Midterm / Molecular Visualization of Structure
Week 7: Protein Structure Analysis
Week 8: RNA Genomics
Week 9: Functional Classification / Review for Final
Week 10: Human Population Analysis / Final