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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 Shift-And-Algorithm
Script String Matching
20.10.2008 Horspool-Algorithm; Tries
27.10.2008 Constructing Suffix Trees from Suffix-Arrays
Please contact Johannes Fischer for an additional copy of the script!
3.11.2008 Linear Time Construction of Suffix- & LCP-Arrays
10.11.2008 Introduction to Support Vector Machines
Folien SVMs I
17.11.2008 String Kernels
Folien SVMs II
24.11.2008 Longest Common Prefixes and Suffixes;
Previous Common Substrings
Please contact Johannes Fischer for an additional copy of the script!
1.12.2008 LZ-factorization; Runs in O(n log n) time
8.12.2008 Runs in O(n) time; Tandem Repeats *
15.12.2008 Motif Finding and the Projection Method
Motif Finding
12.1.2009 Patternbranching; Profilebranching
19.1.2009 Alignments and Segmentation **
Folien Alignments and Segmentation
26.1.2009 Motif Finding and SVMs *** Folien POIMs
Reduction LCA -> RMQ
Please contact Johannes Fischer for an additional copy of the script!
2.2.2009 O(1)-RMQs with O(n) space
9.2.2009 O(1)-RMQs (continued);
Inside Google ****

Bemerkungen zu den mündlichen Prüfungen: (*): ohne 5.8ff; (**): bis Folie 38; (***): nur warum die Interpretation von SVMs schwierig ist; (****): "Inside Google" nicht prüfungsrelevant


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
Exercise set no. 2 get PDF file
Exercise set no. 3 get PDF file
Exercise set no. 4 get PDF file
Exercise set no. 5 get PDF file
Exercise set no. 6 get PDF file
Exercise set no. 7 get PDF file
Exercise set no. 8 get PDF file
Exercise set no. 9 get PDF file
Exercise set no. 10 get PDF file
Exercise set no. 11 get PDF file
Exercise set no. 12 get PDF file
Exercise set no. 13 get PDF file

 

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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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