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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 |
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| 27.10.2008 | Constructing Suffix Trees from Suffix-Arrays |
Please contact Johannes Fischer for an additional copy of the script!
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| 3.11.2008 | Linear Time Construction of Suffix- & LCP-Arrays |
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| 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 |
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| 8.12.2008 | Runs in O(n) time; Tandem Repeats * |
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| 15.12.2008 | Motif Finding and the Projection Method |
Motif Finding |
| 12.1.2009 | Patternbranching; Profilebranching |
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| 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 |
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| 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  |
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Exercise set no. 2 |
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Exercise set no. 3 |
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Exercise set no. 4 |
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Exercise set no. 5 |
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Exercise set no. 6 |
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Exercise set no. 7 |
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Exercise set no. 8 |
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Exercise set no. 9 |
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Exercise set no. 10 |
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Exercise set no. 11 |
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Exercise set no. 12 |
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Exercise set no. 13 |
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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).
