THIS IS STILL OLD

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 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.