Algorithms for Biological Sequence Analysis

Algorithms for Biological Sequence Analysis

DM813, Fall 2009

Daniel Merkle


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 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.


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.

DateTopicReadingWeekly 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


Books used for the Lecture

In addition to the books we will use original articles as a source of information:

Original Articles

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