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 LectureSorted ascending
22.05.-07.06. (Enhanced) Suffix Array and FM-index
23.04.-28.04. Assignment week 1
14.05.-18.05 Assignment week 2
11.06.-15.06 Assignment week 3
10.07.2012 Buffer
07.06.-19.06. Comparative RNA analysis
12.07.2012 Exam
01.05.-08.05. Filter Algorithms
21.06.-03.07. Genome Comparison
01.05.2012 Holiday
31.05.2012 Lecture 10: BWT based string searching and compression
05.06.2012 Lecture 11: Enhanced suffix arrays
07.06.2012 Lecture 12: Comparative RNA Analysis
19.06.2012 Lecture 13: Comparative RNA Analysis II
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
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
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
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
10.04.-17.04. Online Searching and Verification
30.05.2012 Review 1 (during exercises)
05.07.2012 Review 2 (during lecture)

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 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.

OLD CONTENT.

Topic revision: r32 - 12 Mar 2013, KnutReinert
 
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