Algorithms for Biological Sequence Analysis

Algorithms for Biological Sequence Analysis

DM813, Fall 2010

Daniel Merkle

News

06.01.2011: Exam Information online.

06.01.2011: Final slides (including week 50, 51) are online.

01.12.2010: Slides update (week 49/50). Book chapter (Chapter 1 and 2 from [2]) online.

03.12.2010: Chapter 8 from [3] can be found in blackboard. (Chapter 7 can be found on the publishers webpage)

01.12.2010: Slides for week 48 are online.

01.12.2010: Chapter 6 from [3] can be found in blackboard.

23.11.2010: Second mandatory assignment online.

23.11.2010: Weekly notes for week 47 are online.

15.11.2010: Weekly notes for week 46 are online.

13.11.2010: Slides for Chapter 4 and 5 are online.

01.11.2010: Site Launch.

Schedule

All lectures are in the IMADA seminar room. (The schedule might be modified, but I'll try to not have lectures on Fridays).

Lecture 45 46 47 48 49 50 51
Wed 08-10 Lecture Lecture Lecture Lecture Lecture Lecture Lecture
Thu 10-12 Lecture Lecture Lecture Lecture Lecture Lecture (Lecture)
Fri 10-12

Weekly Notes

The slides (and additional material) presented in the lectures can be found in the Blackboard System.

DateTopicReadingWeekly Notes
Week 45 Reading: 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 (BLOSUM); Indexing Techniques, BLAST, FASTA. Multiple sequence alignments. Chapter 5.2-5.4 from [3] and [5] Week 46
Week 47 Cophylogenetics, Coevolution, Tanglegram Layout. Reading: See weekly notes Week 47
Week 48 Patterns, Profiles, and Multiple Sequence Alignments. Chapter 6 from from [3] Week 48
Week 49 Phylogenetics. Selected parts from Chapters 7 and 8 from [3]
Week 50 Continue with Phylogenetics. Start with genome rearrangements. Still Chapters 7 and 8 (focus on Chapter 8) from [3], [6]
Week 51 Continue with genome rearrangements. [6]

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

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

Original Articles

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