Lecture: Computational Sequence Analysis (in English)

 

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.