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 | |
---|---|---|
12.07.2013 | Exam | |
17.05.2013 | Exercise | |
31.06.2013 | Exercise | |
13.06.2013 | Exercise | |
27.06.2013 | Exercise | |
11.07.2013 | Exercise | |
16.04.2013 | Exercise (see Exercise 1) | |
12.04.2013 | Exercise exercise_1+2.pdf | |
26.04.2013 | Exercise exercise_3.pdf | |
30.04.2013 | Exercise exercise_4.pdf | |
16.05.2013 | Exercise exercise_5.pdf | |
30.05.2013 | Exercise exercise_6.pdf | |
14.06.2013 | Exercise exercise_7.pdf | |
28.06.2013 | Exercise exercise_8.pdf | |
09.07.2013 | Exercise exercise_9.pdf | |
07.06.-20.06. | Filtering and approximate search in indices | |
04.07.-12.07 | Genome comparison | |
11.06.2013 | Lecture 10: Filter algorithms and approximate index search | |
25.06.2013 | Lecture 11: RNA I | |
04.07.2013 | Lecture 12: Genome comparison I | |
05.07.2013 | Lecture 13: Genome comparison II | |
09.04.2013 | Lecture 1: Organisation, Rehearsal suffix array construction and search | |
11.04.2013 | Lecture 2: Linear time lcp computation (Kasai) | |
23.04.2013 | Lecture 3: Linear time construction with the SKEW algorithm | |
25.04.2013 | Lecture 4: Lazy suffix trees | |
10.05.2013 | Lecture 5: Enhanced suffix arrays 1 | |
14.05.2013 | Lecture 6: Enhanced suffix arrays 2 | |
24.05.2013 | Lecture 7: BWT 1 | |
28.05.2013 | Lecture 8: BWT 2 | |
07.06.2013 | Lecture 9: Filter algorithms | |
19.04.2013 | Review 1 | |
07.05.2013 | Review 2 | |
23.05.2013 | Review 3 | |
06.06.2013 | Review 4 | |
20.06.2013 | Review 5 | |
02.07.2013 | Review 5 | |
21.06.-25.06. | RNA analysis | |
18.04.2013 | Seminar 1 (A): Two Space Saving Tricks for Linear Time LCP Array Computation (Manzini) | |
02.05.2013 | Seminar 2 (B): DisLex a transformation for discontiguous suffix array construction | |
03.05.2013 | Seminar 3 (A): An incomplex algorithm for fast suffix array construction | |
21.05.2013 | Seminar 5 (A/B): Replacing suffix trees with enhanced suffix arrays | |
04.06.2013 | Seminar 6 (B): High throughput short read alignment via bi-directional BWT | |
18.06.2013 | Seminar 7 (A+B): Masai.pdf | |
23.04.-09.05. | Suffix arrays: construction | |
10.05.-22.05. | Suffix arrays: navigating | |
09.04.-19.04. | Suffix arrays: searching with lcp array | |
24.05.-07.06. | The BWT: searching in the FM index |
Group A | Group B |
---|---|
Phieler | Hesse |
Schmoldt | Martens |
Matzig | Eckert |