BIOC3991C/BIOL3991C Introduction to Molecular Evolution and Bioinformatics
WINTER 2010
GENERAL CLASS INFO
Instructor: Olga Zhaxybayeva (office: Flemington 7 
; email: o l g a z h [at] m t a [dot] c a)
Class Meeting Time and Place: 10:30-11:20 MW (lectures) DUNN 106, F (lab) DUNN 102
Office Hours: M 11:20-12:20, Tue 16:00-17:00 or by appointment
; email: o l g a z h [at] m t a [dot] c a)Class Meeting Time and Place: 10:30-11:20 MW (lectures) DUNN 106, F (lab) DUNN 102
Office Hours: M 11:20-12:20, Tue 16:00-17:00 or by appointment
GRADING CRITERIA
- 30% midterm,
- 30% final,
- 30% homework + computer lab assignments,
- 10% independent mini-project
TEXTBOOK
SUPPLEMENTARY TEXTBOOK
FURTHER READING (General Book Recommendations)
 |
“Essential Bioinformatics” by Jin Xiong , Cambridge University Press 2006 |
SUPPLEMENTARY TEXTBOOK
 |
"Understanding Bioinformatics" by Marketa Zvelebil and Jeremy Baum , Garland Science, 2007 |
FURTHER READING (General Book Recommendations)
LINKS TO LECTURES
- SYLLABUS [PDF]
- CLASS 1. Introduction. Biological Databases.
- CLASS 2. LAB -- Biological Database Search Exercise. [P.S.]
- CLASS 3. Homology. Pairwise Sequence Alignment.
- CLASS 4. BLAST.
- CLASS 5. LAB -- Statistics of Sequence Comparison.
- CLASS 6. Introducing Annotathon.
- CLASS 7. Multiple Sequence Alignment.
- CLASS 8. LAB -- DotLet. [P.S.]
- CLASS 9. Evolution of the Universe and Life.
- CLASS 10. Looking for Distant Homologs.
- CLASS 11. LAB -- Multiple Sequence Alignments.
- CLASS 12. Proteins in Bits and Pieces.
- CLASS 13. An Overview of Prokaryotic Genome Annotation.
- CLASS 14. LAB -- PSI-BLAST.
- CLASS 15. Introns and methods of gene prediction in Eukaryotes.
- CLASS 16. Evaluation of performance. Intro to Phylogenetic Reconstruction.
- CLASS 17. LAB -- Gene Prediction. [P.S.]
- CLASS 18. Cladistics. Types of Homology. Mutations and Substitutions.
- CLASS 19. Cladistics. Types of Homology. Mutations and Substitutions (cont.)
- CLASS 20. LAB -- Genome-wide Online Analyses.
- CLASS 21. REVIEW.
- CLASS 22 (March 3rd). MIDTERM.
- CLASS 23. LAB -- Biology WorkBench and CAMERA.
- CLASS 24. Substitution Models. Tree Reconstruction Methods (Overview)
- CLASS 25. Bootstrapping. Long Branch Attraction. Concept of an Outgroup. Neighbor-Joining Trees.
- CLASS 26. LAB -- Phylogenetic Trees with CLUSTALX and NJPLOT.
- CLASS 27. ASRV. Consensus Trees. Exploration of Tree Space. Parsimony. PHYLIP.
- CLASS 28. Tree of Life.
- CLASS 29. LAB -- Distance, Parsimony and ML phylogenetic analyses. Long Branch Attraction.
- CLASS 30. Maximum Likelihood and its applications.
- CLASS 31. Bayesian Methods.
- CLASS 32. Selection and Neutral Evolution.
- CLASS 33. REVIEW.