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BCH441 - Bioinformatics

Welcome to the BCH441 Course Wiki.

This is our main tool to coordinate information, activities and projects in University of Toronto's bioinformatics course BCH441. If you are not one of our students, you can still browse this site, however only users with a login account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.

The Course

I am in the process of repairing the original course Wiki and many of the pages are still arbitrarily outdated. Please don't use pages other than those that are linked directly from here.
Contact Boris Steipe for all matters of urgency. November 11. 2011

Assignments

Assignment 4 has been posted.
Due Monday, Nov. 28.

Temporary links for material

Lecture slides

• 01 - Introduction to the course (pdf, 6.1 MB)
• 02 - Sequence Data (pdf, 4.6 MB)
• 03 - Structure Data (pdf, 13.6 MB)
• 04 - Sequence Analysis I (pdf, 8.6 MB)
• 05 - Sequence Analysis II (pdf, 3.1 MB)
• 06 - Interpreting Protein Structure (pdf, 6.6 MB)
• 07 - Structural Domains (pdf, 5.8 MB)
• 08 - Genome Sequencing
• 09 - Genome Annotation (pdf, 4.2 MB)
• 10 - Homology I: Principles (pdf, 2.6 MB)
• 11 - Homology II: Optimal Sequence Alignment (pdf, 2.6 MB)
• 12 - Homology III: BLAST (pdf, 2.6 MB)
• 13 - Homology IV: Multiple Sequence Alignment (pdf, 4.3 MB)
• 14 - Predicting Protein Structure I: Homology Modeling (pdf, 2.3 MB)
• 15 - Phylogenetic Analysis I (pdf, 3.3 MB)
• 16 - Phylogenetic Analysis II
• 17 - Comparative Genomics
• 18 - Computational Systems Biology
• 19 - Structure Prediction II: ab initio Prediction
• 20 - Statistics and Exploratory Data Analysis
• 21 - Gene regulation
• 22 - Metabolic Pathways

Lecture recordings

• Thursday, 15. September 2011: Lecture 02 (Sequence data) (mp4, 16.4 MB)
• Monday, 19. September 2011: Lecture 03 (Sequence data cont.; Structure Data) (mp4, 17.2 MB)
• Thursday, 22. September 2011: Lecture 04 (Structure data cont.; Sequence Analysis I) (mp4, 16.9 MB)
• Monday, 26. September 2011: Lecture 05 Sequence Analysis I cont. & II (mp4, 15.3 MB)
• Thursday, 29. September 2011: Lecture 06 Sequence Analysis II cont. & Analysis of structure (mp4, 15.6 MB)
• Monday, 3. October 2011: Analysis of Structure (cont.) (mp4, 18.3 MB)
• Thursday, 6. October 2011: Lecture 07 Protein Structural Domains (mp4, 16.3 MB)
• Thursday, 13. October 2011: (Parkinson)
• Monday, 17. October 2011: (Parkinson)
• Thursday, 20. October 2011: Lecture 10 Homology I: Principles (mp4, 19.4 MB)

• Monday, 24. October 2011: Lecture 11 Homology II: Optimal Sequence Alignment (mp4, 12.4 MB)
• Thursday, 27. October 2011: Lecture 12 Homology III: BLAST (mp4, 16.8 MB)
• Monday, 31. October 2011: Lecture 13 Homology IV: Multiple Sequence Alignment (mp4, 22.7 MB)
• Thursday, 3. November 2011: Lecture 14 Predicting Protein Structure I: Homology Modeling (mp4, 18.7 MB)
• Thursday, 10. November 2011: Lecture 15 Phylogenetic Analysis I: Principles (mp4, 16.7 MB)

• Monday, 14. November 2011: Lecture 16 Phylogenetic Analysis II (Quiz 3)
• Thursday, 17. November 2011: Lecture 17 Comparative Genomics (Parkinson)
• Monday, 21. November 2011: Lecture 18 Computational Systems Biology (Parkinson) (Quiz 4)
• Thursday, 24. November 2011: Lecture 19 Protein structure prediction II: ab initio
• Monday, 28. November 2011: Lecture 20 Exploratory Data Analysis
• Thursday, 1. December 2011: Lecture 21 Gene Regulation
• Monday, 6. December 2011: Lecture 22 Metabolic Pathways (Quiz 5)
• Virtual Monday, 7. December 2011: Exam review