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 |
Practical exercises |
during assignment weeks Tue, Thu |
10-12 |
A2 |
Bioinformatik pool |
Exercise |
Wed |
14-16 |
Arnimallee 14 |
HS B (0.1.0.1) |
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.