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Lecture: Bioinformatics I
| Lecturers | Prof. Dr. Daniel Huson, Dr. Johannes Fischer and Dr. Stefan Henz |
| Lectures | Mondays 9-11 A301, Sand 1, Wednesdays 12-14, Kleiner Hörsaal, Sand 6/7 |
| Problem sessions |
Group A: Tuesdays 14:15 - 15:45, C118, Sand 14. Group B: Tuesdays 15:00 - 16:30, Seminarraum F116, Sand 6/7. no sessions on 15.12.09 |
| Target audience |
Diploma- and master-students |
| Modules |
See "Modulhandbuch" |
| Language |
English |
Contents
Bioinformatics I focuses on concepts, data-structures and algorithms for sequence analysis.
| Date |
Contents |
|---|---|
| 19.10.2009 | 1. Introduction; 2. Pairwise Alignment: Hirschberg |
| 21.10.2009 | Hirschberg-Alignment (ctd.) |
| 26.10.2009 |
Gotoh-Algo; 3. Multiple Sequence Alignment (MSA) |
| 28.10.2009 | MSAs with ILPs (ctd.) |
| 2.11.2009 | Optimal MSA; Progressive Alignment; ClustalW; MUSCLE; T-Coffee; DIALIGN; Consensus Sequences; Profiles and Motifs; TransFac; SeqLogos |
| 4.11.2009 | 4. BLAST; BLAT |
| 9.11.2009 | BLAT (ctd.); 5. FASTA |
| 11.11.2009 | 6. Phylogeny: Introduction; Newick format |
| 16.11.2009 | Neighbor-Joining; Jukes-Cantor-Model |
| 18.11.2009 |
continued |
| 23.11.2009 | continued |
| 25.11.2009 | continued |
| 30.11.2009 | 7. Suffix trees |
| 2.12.2009 |
continued |
| 7.12.2009 |
continued |
| 9.12.2009 | 8. Motif finding |
| 14.12.2009 | Mid-term exam |
| 16.12.2009 | 9. HMMs |
| 11.1.2010 | continued |
| 13.1.2010 | 6. Gene finding |
| 18.1.2010 | 10. SVMs + |
| 20.1.2010 |
continued + |
| 25.1.2010 | 11. Physical mapping |
| 27.1.2010 | continued |
| 1.2.2010 | 12. Sequencing and assembly |
| 3.2.2010 | continued |
| 8.2.2010 | 13. Population genetics + |
| 10.2.2010 | continued + |
| 15.2.2010 | Repetitorium |
| 17.2.2010 | Final exam |
Assignments
- Assignment 1
- Assignment 2
- Assignment 3 (corrected)
- Assignment 4 (the section numbers refer to the handout in the lecture!)
Scripts
- Pairwise Sequence Alignment (not 2.2, 2.3, 2.6, 2.7)
- Multiple Sequence Alignment
- Multiple Sequence Alignment Part II (not 3.8)
- BLAST and BLAT
- FASTA
- Phylogeny I
- Phylogeny II
Recommended textbooks (but none covers the whole course)
- Neil C. Jones, Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms. MIT Press, 2004.
- Dan Gusfield: Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge UP, 1997.
- Richard Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge UP, 1998.
- Pierre Baldi, Soren Brunak: Bioinformatics: The Machine Learning Approach. MIT Press, 1998.
How to get credit for this course:
• Always participate in the weekly problem sessions and present your results regularly.
• Pass the mid-term exam
• Pass the final exam
You may work on and hand-in assignments in groups of up to two people.
Grade determined as follows: 1/3 assignments, 1/3 mid-term exam, 1/3 final exam
