News
17.12.2009: Details for the oral exam on January, 8th are online. If you want to register for a specific slot, you can do it until Friday (Dec., 18th, 12am) in the IMADA secretary's office (or my office). Otherwise you will be just scheduled.
16.12.2009: Weekly Notes for week 51 are online.
15.12.2009: Chapter 8 of [4] is available in the Blackboard System (will be discussed in Week 51).
09.12.2009: Weekly Notes for week 50 are online.
01.12.2009: Second Mandatory Assignment: The workspace for
CoRe-PA to be imported in Eclispe
(file core-pa_0.3a_workspace.zip in the
Blackboard System) was updated. There is only a small
modification. The current version does not require to move any
libraries or to set pathnames for libraries in the source code
explicitly.
01.12.2009: Weekly Notes for week 49 are online.
26.11.2009: The ILP formulation (Blackboard System) was slightly updated (weights are now included), the slide set "Short Recap of (Integer) Linear Programming" was uploaded.
26.11.2009: The second mandatory assignment was published. Note, that a timeout mechanism for the GLPK solver was included (set to 30 seconds, feel free to change this). The source code of CoRe-PA is available via the Blackboard System. Deadline for the second assignment is Wednesday, December, 30th, 10:00.
25.11.2009: New files is the Blackboard System: Slide set for week 48, several files for mandatory assignment 2. The sources of CoRe-PA will be uploaded Thursday, Nov. 26th. The example files will be used in the lecture on Thursday.
23.11.2009: Weekly Notes for week 48 are online. Note that it includes a link to the preliminary description of mandatory assignment 2.
16.11.2009: Weekly Notes for week 47 are online.
09.11.2009: Weekly Notes for week 46 are online.
05.11.2009: First mandatory assignment was published.
29.10.2009: Weekly Notes for week 45 are online.
27.10.2009: The Weekly Notes for week 45 will be published end of this week. Note however that you are not requested to buy a course book, as the material needed will be provided.
23.10.2009: Site Launch.
Schedule
Next meeting: Thursday, 10/12, at 10:15, IMADAs Seminar Room
Weekly Notes
The slides (and additional material) presented in the lectures can be found in the Blackboard System.
| Date | Topic | Reading | Weekly Notes |
|---|---|---|---|
| Week 45 | Central Dogma, Scoring Matrices, Local and Global Sequence Alignment, Smith-Watermann, Needleman-Wunsch | Chapters 1, 4.1, 5.1, and 5.2 from [3] | Week 45 |
| Week 46 | Substitution and scoring matrices, PAM, BLOSUM; Indexing Techniques, BLAST, FASTA | Chapter 5.1 and 5.3 from [5] | Week 46 |
| Week 47 | Indexing Techniques, BLAST, FASTA | Chapter 1 from [4] + original articles (see Weekly Notes) | Week 47 |
| Week 48 | Coevolution, Tanglegram Layout | see Weekly Notes, [4] | Week 48 |
| Week 49 | Coevolution, Genome Rearrangements | [2], details see Weekly Notes | Week 49 |
| Week 50 | Reversal Median Problem, Phylogenetics | Chapter 7 from [3], see Weekly Notes | Week 50 |
| Week 51 | Phylogenetics | Chapter 8 from [3] | Week 51 |
Office Hours
Just write a short mail, and come by.
- Office: IMADA, Ø14-602b-2 map.
- Phone: 2322
- E-mail: daniel
Literature
Books used for the Lecture
- [1] Bioinformatics and Functional Genomics, 2009, Second Edition, by Jonathan Pevsner
- [2] Combinatorics of Genome Rearrangements, 2009, by Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier and Stéphane Vialette
- [3] Understanding Bioinformatics, 2008 by Marketa Zvelebil and Jeremy O. Baum, Chapter 1, Chapter 4, Chapter 7
- [4] Tangled Trees - Phylogeny, Cospeciation, and Coevolution, 2003, edited by Roderic D. M. Page
In addition to the books we will use original articles as a source of information:
Original Articles
- [5] BLOSUM62 miscalculations improve search performance. Mark P Styczynski; Kyle L Jensen, Isidore Rigoutsos, Gregory Stephanopoulos (2008). Nat. Biotech. 26: 274-275. doi:10.1038/nbt0308-274.