BME110: Computational Biology Tools
Spring 2005
Tue/Thur 2-3:45pm
Baskin Engineering 156
| Instructors: |
|
Todd Lowe
Email: lowe @ soe.ucsc.edu
Office: 227 Sinsheimer
Phone: 459-1511
Office Hours:
Tues 1-2pm, Thurs 4-5pm
|
Elizabeth Corey
Email: ecorey @soe.ucsc.edu
Office: 309B Baskin Engineering
Office Hours: Thurs 1-2pm
|
Syllabus
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 @soe.ucsc.edu)
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 |
Grading:
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
- genome browsers
- NCBI tools
- other bioinformatics databases
- sequence formats
- sequence databases
Week 2: Single Sequence Analysis
- basic gene structure
- translating DNA sequences
- basic DNA analysis: restriction sites, primer design, GC content,
codon usage
- calculating protein physical properties
- protein sequence motifs
- local structure prediction
Week 3: Pairwise Sequence Comparison, BLAST
- Dot plots
- Global and local alignment
- BLAST
- Scoring matrices, gap penalties, evolutionary distance
- statistical significance
Week 4: Sensitive Protein Searching
- BLASTP
- PSI-BLAST
- PSSMs
- HMMs
- Fold recognition
Week 5: Multiple Sequence Alignment & Phylogenetics
- Progressive vs. heirarchical methods
- Tcoffee, clustalW
- Viewing and editing alignments
- Building trees, various methods
- Visualizing trees
Week 6: Midterm / Molecular Visualization of Structure
- Structure databases
- Visualizing RNA and protein structures
Week 7: Protein Structure Analysis
- assessing structure quality
- analyzing structural properties: secondary structure, hydrogen
bonds, molecular surfaces
- structure-structure superposition
- structure classification systems
Week 8: RNA Genomics
- Structure comparison & classification
- Structure-based alignments
- RNA features, predicting secondary structure
- RNA databases
- RNA motif searching
- Specialized RNA gene finding
- Generalized RNA gene finders
Week 9: Functional Classification / Review for Final
- COGS database
- finding orthologs and paralogs
- Gene ontology
- Pathway Databases
Week 10: Human Population Analysis / Final
- SNP databases
- High-throughput genotyping
- Population analysis
- Application to health & medicine