Welcome to the Wiki of the Lecture Sequence Analysis. This module consists of 2 hours lecture, 2 hours exercise and 2 hours seminar. The form will be in blocks, in which you will hear about certain aspects of sequence analysis in the lecture, then in the ecercises you will work out details prepare for the seminar.
In the seminar we will all talk about an original paper connected to the topic (discussion leaders will be chosen by a draw) and afterwards have a short review exam for the block. Students will be in two groups (A and B) which will take turn in giving seminar talks.
Each block is finished by a review.
For the exam the content of the seminar papers AND lectures will be relevant.
Event | Day | Time | Address | Room |
---|---|---|---|---|
Lecture (until June 4th) | Tuesday | 10-12 | Takustr. 9 | SR 005 |
Lecture (after June 4th) | Tuesday | 10-12 | Arnimallee 6 | SR 032 |
Exercise (until June 6th) | Thursday | 10-12 | Takustr. 9 | SR 005 |
Exercise (after June 6th) | Thursday | 10-12 | Takustr. 9 | SR 053 |
Seminar | Friday | 14-16 | Takustr. 9 | SR 005 |
Date | Lecture | |
---|---|---|
24.05.-07.06. | The BWT: searching in the FM index | |
09.04.-19.04. | Suffix arrays: searching with lcp array | |
10.05.-22.05. | Suffix arrays: navigating | |
23.04.-09.05. | Suffix arrays: construction | |
18.06.2013 | Seminar 7 (A+B): Masai.pdf | |
04.06.2013 | Seminar 6 (B): High throughput short read alignment via bi-directional BWT | |
21.05.2013 | Seminar 5 (A/B): Replacing suffix trees with enhanced suffix arrays | |
03.05.2013 | Seminar 3 (A): An incomplex algorithm for fast suffix array construction | |
02.05.2013 | Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction | |
18.04.2013 | Seminar 1 (A): Two Space Saving Tricks for Linear Time LCP Array Computation (Manzini) | |
21.06.-25.06. | RNA analysis | |
20.06.2013 | Review 5 | |
02.07.2013 | Review 5 | |
06.06.2013 | Review 4 | |
23.05.2013 | Review 3 | |
07.05.2013 | Review 2 | |
19.04.2013 | Review 1 | |
07.06.2013 | Lecture 9: Filter algorithms | |
28.05.2013 | Lecture 8: BWT 2 | |
24.05.2013 | Lecture 7: BWT 1 | |
14.05.2013 | Lecture 6: Enhanced suffix arrays 2 | |
10.05.2013 | Lecture 5: Enhanced suffix arrays 1 | |
25.04.2013 | Lecture 4: Lazy suffix trees | |
23.04.2013 | Lecture 3: Linear time construction with the SKEW algorithm | |
11.04.2013 | Lecture 2: Linear time lcp computation (Kasai) | |
09.04.2013 | Lecture 1: Organisation, Rehearsal suffix array construction and search | |
05.07.2013 | Lecture 13: Genome comparison II | |
04.07.2013 | Lecture 12: Genome comparison I | |
25.06.2013 | Lecture 11: RNA I | |
11.06.2013 | Lecture 10: Filter algorithms and approximate index search | |
04.07.-12.07 | Genome comparison | |
07.06.-20.06. | Filtering and approximate search in indices | |
09.07.2013 | Exercise exercise_9.pdf | |
28.06.2013 | Exercise exercise_8.pdf | |
14.06.2013 | Exercise exercise_7.pdf | |
30.05.2013 | Exercise exercise_6.pdf | |
16.05.2013 | Exercise exercise_5.pdf | |
30.04.2013 | Exercise exercise_4.pdf | |
26.04.2013 | Exercise exercise_3.pdf | |
12.04.2013 | Exercise exercise_1+2.pdf | |
16.04.2013 | Exercise (see Exercise 1) | |
17.05.2013 | Exercise | |
31.06.2013 | Exercise | |
13.06.2013 | Exercise | |
27.06.2013 | Exercise | |
11.07.2013 | Exercise | |
12.07.2013 | Exam |
Group A | Group B |
---|---|
Phieler | Hesse |
Schmoldt | Martens |
Matzig | Eckert |