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
7	Exercise7.pdf
6	Exercise6.pdf
5	Exercise5.pdf
4	Exercise4.pdf
3	Exercise3.pdf
2	Exercise2.pdf
1	Exercise1.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.