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
Reviews
Results Review1
Results Review2
Requirements 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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