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Page AdvancedAlgorithms12
Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4).
News
- (18.1.13) The results of the second exam can be found below
- (24.9.12) The second exam will take place on Wednesday 24.10.12 12-14 in room SR119, Arnimallee 3
- (14.3.12) The lecture this year will be interleaved with practical exercises that will take place in the Bioinformatik pool.
Results exam 2
| Matrikelnummer | points | mark |
|---|---|---|
| xxx343 | 74.5 | 1.3 |
| xxx956 | 33 | 5.0 |
| xxx8987 | 51 | 3.3 |
| xxx3988 | 12 | 5.0 |
| xxx4170 | 39.5 | 4.0 |
| xxx8601 | 47 | 3.3 |
| xxx539 | 38 | 4.0 |
| xxx2779 | 51 | 3.3 |
Results exam
| Matrikelnummer | points | mark |
|---|---|---|
| xxx9094 | 62 | 2.3 |
| xxx4048 | 39 | 4.0 |
| xxx9983 | 0 | 5.0 |
| xxx6803 | 44 | 3.7 |
| xxx343 | 0 | 5.0 |
| xxx2343 | 0 | 5.0 |
| xxx2041 | 0 | 5.0 |
| xxx5236 | 60.5 | 2.3 |
| xxx938 | 0 | 5.0 |
| xxx4884 | 72.5 | 1.7 |
| xxx1290 | 50 | 3.3 |
| xxx956 | 24 | 5.0 |
| xxx2428 | 0 | 5.0 |
| xxx6387 | 0 | 5.0 |
| xxx7470 | 55.5 | 3.0 |
| xxx5642 | 73 | 1.7 |
| xxx1170 | 60.5 | 2.3 |
| xxx5132 | 71 | 1.7 |
| xxx6675 | 58 | 2.7 |
| xxx8987 | 0 | 5.0 |
| xxx9136 | 55 | 3.0 |
| xxx6571 | 72 | 1.7 |
| xxx1655 | 61 | 2.3 |
| xxx8462 | 58.5 | 2.7 |
| xxx1786 | 61 | 2.3 |
| xxx3988 | 30 | 5.0 |
| xxx480 | 60.5 | 2.3 |
| xxx671 | 83 | 1.0 |
| xxx1347 | 69.5 | 1.7 |
| xxx2077 | 70.5 | 1.7 |
| xxx5795 | 61.5 | 2.3 |
| xxx4170 | 19 | 5.0 |
| xxx7727 | 55 | 3.0 |
| xxx3962 | 61.5 | 2.3 |
| xxx4177 | 69.5 | 1.7 |
| xxx6835 | 66 | 2.0 |
| xxx6104 | 73 | 1.7 |
| xxx3282 | 27 | 5.0 |
| xxx1695 | 58 | 2.7 |
| xxx2290 | 78 | 1.0 |
| xxx7304 | 60.5 | 2.3 |
| xxx6942 | 65 | 2.0 |
| xxx7315 | 0 | 5.0 |
| xxx8601 | 0 | 5.0 |
| xxx539 | 0 | 5.0 |
| xxx6179 | 71.5 | 1.7 |
| xxx4859 | 75.5 | 1.3 |
| xxx7592 | 54 | 3.0 |
| xxx1288 | 41 | 4.0 |
| xxx2779 | 29 | 5.0 |
Times and rooms
Rooms and timings
| Event | Day | Time | Address | Room |
|---|---|---|---|---|
| Lecture | Tue | 10-12 | Takustr. 9 | 005 |
| Lecture | Thu | 10-12 | Takustr. 9 | 005 |
| Exercise | Wed | 14-16 | Arnimallee 14 | HS B (0.1.0.1) |
| Practical exercises | during assignment weeks Tue, Thu | 10-12 | A2 | Bioinformatik pool |
Schedule
| Date | Lecture | |
|---|---|---|
| 10.04.-17.04. | Online Searching and Verification | |
| 10.04.2012 | Lecture 1: Introduction, simple Horspool and Wu-Manber algorithm | |
| 12.04.2012 | Lecture 2: Shift-Or algorithm, Ukkonen trick for approximate string matching | |
| 17.04.2012 | Lecture 3: Myers bitvector edit distance algorithm, banded version | |
| 23.04.-28.04. | Assignment week 1 | |
| 01.05.-08.05. | Filter Algorithms | |
| 01.05.2012 | Holiday | |
| 03.05.2012 | Lecture 4: Read mapping considerations | |
| 08.05.2012 | Lecture 5: Pigeonhole filter and q-gram counting filter | |
| 10.05.2012 | Lecture 6: q-gram counting filter II | |
| 14.05.-18.05 | Assignment week 2 | |
| 22.05.-07.06. | (Enhanced) Suffix Array and FM-index | |
| 22.05.2012 | Lecture 7: Suffix array construction and searching with lcp values | |
| 24.05.2012 | Lecture 8: Suffix array construction in linear time | |
| 29.05.2012 | Lecture 9: Burrows-Wheeler transform (BWT), L-to-F mapping | |
| 30.05.2012 | Review 1 (during exercises) | |
| 31.05.2012 | Lecture 10: BWT based string searching and compression | |
| 05.06.2012 | Lecture 11: Enhanced suffix arrays | |
| 07.06.-19.06. | Comparative RNA analysis | |
| 07.06.2012 | Lecture 12: Comparative RNA Analysis | |
| 11.06.-15.06 | Assignment week 3 | |
| 19.06.2012 | Lecture 13: Comparative RNA Analysis II | |
| 21.06.-03.07. | Genome Comparison | |
| 21.06.2012 | Lecture 14: Collinear genome comparison I: Segment match refinement | |
| 26.06.2012 | Lecture 15: Collinear genome comparison II: Multiple semgent match refinement and T-Coffee | |
| 28.06.2012 | Lecture 16: Non-collinear alignment: progressiveMauve | |
| 03.07.2012 | Lecture 17: Genome rearrangement | |
| 05.07.2012 | Review 2 (during lecture) | |
| 10.07.2012 | Buffer | |
| 12.07.2012 | Exam | |
Exercises
| Nr. | Link |
|---|---|
| 1 | Exercise1.pdf |
| 2 | Exercise2.pdf |
| 3 | Exercise3.pdf |
| 4 | Exercise4.pdf |
| 5 | Exercise5.pdf |
| 6 | Exercise6.pdf |
| 7 | Exercise7.pdf |
Reviews
Results Review1 Results Review2Requirements for Aktive Teilnahme
You have to hand in 75% of all practical assignments. (You have to show reasonable programs and can explain them.)In addition you need to reach 50% of all points of the two reviews.
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