Classified as:	Practical Computer Science
Lecturer:	Prof. Daniel Huson
Location of Lecture:	Lecture theater 2, Sand 6/7
Time of Lecture:	Thursdays, 15:15-17h
Tutor:	Tobias Dezulian
Tutorial: Time & Place:	Thu, 17:15 - 18:15, A104 , Sand 1, starting Nov 25.
Office hours:	Daniel Huson: Thursdays, 17-18h and by appointment, C310a Tobias Dezulian: drop-in or by appointment
Requirements for admission:	Vordiplom

Some sections of this course are based on lectures prepared by Prof. Knut Reinert and Clemens Groepl for a course on "Advanced Aspects in Sequence Analysis" that they taught at the FU-Berlin in the summer semester of 2004. Section 4 is based on lecture notes written by Prof. Enno Ohlebusch in Ulm.

Contents and Script:

- 0. Introduction
- 1 Fast string matching
- 2. Multiple string matching
- 3. Bit vector based approximate string matching *
- 4. Suffix arrays and suffix trees
- 5. Jumping alignments
- 6. MSA using DCA and branch-and-bound +
- 7. Motive finding +
- 8. Multiple genome alignment *
- 9. HCS genome comparison *
- 10. Segment match refinement *
- 11. Optimal syntenic layout *

*) These chapters will not be part of the oral exam.
+) If you are taking a 2+1 exam, then DCA (Chapter 6) and the projection method (Chapter 7) will be part of the exam, otherwise not.

Literature:

As listed in the script

Assignments:

Assignments#1-3
Assignments#4
Assignments#5
Assignments#6-7
Assignments#8-9 WINNOWER paper Cliquer Cliquer documentation
Assignments#10
Assignments#11 human.fa mouse.fa CGViz_human_mouse_matches.cgv CGViz_Examples.zip
Assignments#12

Requirements:

For students in their 5. semester or higher., with "Vordiplom".

Credits for problem sessions:

To obtain credits for attending the problem sessions, you are required to regularly and actively participate in the problem sessions. Additionally, you must regularly hand in assignment sheets and obtain at least 60 % of all possible assignment points. Students are permitted to work in groups of up to two people per group.