Algorithms for Biological Sequence Analysis

Algorithms for Biological Sequence Analysis

DM813, Fall 2012

Daniel Merkle


25.12.2012: Details for the oral exam on January,11th are online.

17.12.2012: Link for Chapter 7 in weekly notes for week 50 fixed.

26.11.2012: Preliminary second mandatory assignment was published.

15.11.2012: The score in Testcase 3 (global alignment) was wrong. I added the correct solution.

06.11.2009: First mandatory assignment was published.

06.11.2012: Access to the Blackboard material is provided via WebDav folders. See the Weekly Notes for how to access the material.

05.11.2012: Site Launch.


All lectures are in the IMADA seminar room. (The schedule might be modified.)

Lecture 45 46 47 48 49 50 51
Tue 10-12 Lecture Lecture Lecture Lecture Lecture Lecture Lecture
Thu 16-18 Lecture Lecture Lecture (Lecture)
Fri 12-14 Lecture Lecture Lecture (13:15 - 14:00) Lecture (12:15 - 13:00)

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 [3] Week 46
Week 47 Coevolution, Dynamic Programming for coevolution reconstructions, ILP formulation for tanglegram layout, ILP formulation for fixing estimated orthology matrices Chapter 1 from [3] + original articles (see Weekly Notes) Week 47
Week 48 Coevolution, orthology relations, gene and species tree reconciliation, an ILP formulation for fixing estimated orthology matrices, Pattern Profiles and Multiple Alignments see Weekly Notes, Chapter 6 from [3] Week 48
Week 49 Hidden Markov Models, Genome Rearrangements - PQ Trees / Sorting / Median Problem [3], details see Weekly Notes Week 49
Week 50 Reversal Median Problem, Phylogenetics (distance correction) Chapter 7 and 8 from [3], see Weekly Notes Week 50
Week 51 Phylogenetics, inferring phylogenetic trees, parsimony and likelihood methods Chapter 8 from [3] tba

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 (see blackboard).

Original Articles

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