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Advanced Methods in Sequence Analysis

        Lecture: Advanced Methods for Sequence Analysis

 

General Information

Lecturer Prof. Dr. Daniel Huson and Dr. Johannes Fischer and Dr. Gunnar Rätsch
Lectures  Mondays, 15:15-17:00, Kleiner Hoersaal, Sand 6/7
Tutorials
Wednesdays, 12:00-13:30, Kleiner Hoersaal, Sand 6/7
Credits 4 LP, 2+2 SWS
Prerequisites
Grundlagen der Bioinformatik or preferably Algorithms in Bioinformatics I-II
Modules
See "Modulhandbuch"
Language
English

Schedule

13.10.2008 String Matching I Skript String Matching
20.10.2008 String Matching II
27.10.2008 Suffix Arrays and Suffix Trees I Skript Suffix Trees
3.11.2008 Suffix Arrays and Suffix Trees II
10.11.2008 Support Vector Machines I Folien SVMs I
17.11.2008 Support Vector Machines II Folien SVMs II
24.11.2008 Finding Repetitive Structures with Suffix Trees I

1.12.2008 Finding Repetitive Structures with Suffix Trees II
8.12.2008 Finding Repetitive Structures with Suffix Trees III
15.12.2008 Motif Finding I
12.1.2009 Motif Finding II
19.1.2009 Motif Finding and SVMs, Lowest Common Ancestors in Trees I

26.1.2009 Lowest Common Ancestors in Trees II

2.2.2009 Alignments and Segmentation
9.2.2009 TBA

Assignments:

Assignments will be posted on this website on Tuedays, to be handed in at the beginning of the lecture on the following Monday.

Exercise set no. 1 get PDF file Solutions 1 get PDF file
Exercise set no. 2 get PDF file Solutions 2 get PDF file Note: Exercise 2(b) is canceled!!!
Exercise set no. 3 get PDF file Solutions 3 get PDF file Exercise 3 should be "less than or equal to"
Exercise set no. 4 get PDF file Solutions 4 get PDF file
Exercise set no. 5 get PDF file

Exercise set no. 6 get PDF file

Credits for this course:

This course is worth 4 LP, so you will be expected to do 4x30=120 hours of work for this course. You are welcome to discuss the problems among each other, but every participant must hand in their own solutions to be graded.

Master students:

You have to take part in the problem sessions and have to hand in solutions to the problem sheets. This grade will make up 20% of your final grade. The final exam (oral) will contribute 80% toward your final grade.

Diploma students:

To get credit for this course, you must obtain 60% of the points from the exercises, both before and after X-mas. There are 8 assigments to hand in before X-mas (so you need at least 70 points), and probably 4 after X-mas (35 points).

Diese Veranstaltung ist prüfbar als Praktische Informatik (2+2 SWS) or Theoretische Informatik (maximal 2+2 SWS).

 

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